Transcription factors (TFs) and the regulatory proteins that control them play key roles in hematopoiesis, controlling basic processes of cell growth and differentiation; disruption of these processes may lead to leukemogenesis. Here we attempt to identify functionally novel and partially characterized TFs/regulatory proteins that are expressed in undifferentiated hematopoietic tissue. We surveyed our database of 15 970 genes/expressed sequence tags (ESTs) representing the normal human CD34+ cells transcriptosome (http://westsun.hema.uic.edu/cd34.html), using the UniGene annotation text descriptor, to identify genes with motifs consistent with transcriptional regulators; 285 genes were identified. We also extracted the human homologues of the TFs reported in the murine stem cell database (SCdb; http://stemcell.princeton.edu/), selecting an additional 45 genes/ESTs. An exhaustive literature search of each of these 330 unique genes was performed to determine if any had been previously reported and to obtain additional characterizing information. Of the resulting gene list, 106 were considered to be potential TFs. Overall, the transcriptional regulator dataset consists of 165 novel or poorly characterized genes, including 25 that appeared to be TFs. Among these novel and poorly characterized genes are a cell growth regulatory with ring finger domain protein (CGR19, Hs.59106), an RB-associated CRAB repressor (RBAK, Hs.7222), a death-associated transcription factor 1 (DATF1, Hs.155313), and a p38-interacting protein (P38IP, Hs. 171185). The identification of these novel and partially characterized potential transcriptional regulators adds a wealth of information to understanding the molecular aspects of hematopoiesis and hematopoietic disorders.

Subjects:
Gene Expression, Hematopoiesis and Stem Cells
Topics:
cd34 antigens, genes, mice, transcription factor, stem cells, regulatory protein

Transcription factors (TFs) play a critical role in the process of lineage commitment and differentiation in hematopoietic tissue.1-4 Several such factors are known to control the basic molecular mechanisms that underlie this process, and their expression is tightly regulated in a stage- and lineage-specific manner.5 For example, the level of expression of PU.1 and GATA binding proteins plays a major regulatory role in myeloid development, with PU.1 being up-regulated with myeloid differentiation,6 whereas GATA1 and GATA2 are down-regulated.6,7 Disruption in the expression, sequence, or structure of critical TFs or their associated regulatory proteins can upset the delicate balance between proliferation and differentiation and lead to leukemogenesis. Most of the consistent translocations in myeloid leukemias that have been analyzed to date result in a fusion protein that alters the normal function of a TF or a related regulatory protein8,9; it is increasingly recognized that these genes might also contribute to leukemia by functional inactivation by mutation10 or chromosomal translocation.11-13 It has been speculated that the majority of translocations that have not yet been fully characterized probably also involve transcriptional regulatory proteins.14-16 Thus, the identification of novel transcriptional regulators, especially those that are located near translocation breakpoints, may help to specify new leukemia-related proteins, leading to better understanding and treatment of this disease.

In the present study, we took a global approach to identify novel and known transcriptional regulators that might participate in hematopoiesis and leukemogenesis by surveying databases of genes that are expressed in normal hematopoietic stem cells. We searched our previously reported database of 15 970 transcripts that are present in human bone marrow CD34 antigen–positive cells17 to identify those with functional motifs consistent with transcriptional regulators. We also searched a murine stem cell database18to find the human homologues of TFs expressed in this tissue. Here we report the results of our search, which identified 330 genes that are potential transcriptional regulators, including 106 TFs, of which 25 are novel or poorly characterized. These TFs, especially those novel ones that have not been reported previously, may represent new pathways in hematopoiesis or leukemogenesis that have not yet been explored.

The human CD34+ transcriptosome database

The preparation of the human CD34+ transcriptosome database was previously reported.17 The database, which is available online at http://westsun.hema.uic.edu/cd34.html, contains 15 970 complementary DNAs (cDNAs) expressed in CD34+cells, and includes the GenBank accession number, the UniGene cluster identification number (http://www.ncbi.nlm.nih.gov/UniGene/) to which the GenBank clone belongs, its relative expression in CD34+ cells, the gene name, a functional description of the gene (from the UniGene text descriptor, build version 129), and its chromosomal location. The UniGene text descriptors of this database were searched for the following terms: transcription factor, leucine zipper, zinc finger, ring finger, helix-loop-helix, PHD, POU, forkhead, bromodomain, homeobox, oncogene, nuclear, activator, and repressor. The dataset was then updated to the most recent UniGene Build version (version 135, June 2001). Redundant cDNAs contained within the same UniGene cluster were removed, saving only the clone having the highest expression level in the CD34+ database. Each cDNA sequence was then used to search the GenBank NR database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide) using BlastN alignment software, to verify homology to the predicted gene, using an arbitrary cut-off of E <-40 to indicate sufficient sequence identity. If the E value was greater than e-40, then the cDNA sequence was also used to search the TIGR database (http://www.tigr.org/) to verify that it is represented by a TIGR contig containing the transcript of the predicted functions. The cDNAs that did not pass these GenBank or TIGR screens were removed from the database, as were genes of known function that clearly did not represent the categories that were being sought.

The murine stem cell database

A murine stem cell database (http://stemcell.princeton.edu) consisting of expressed genes (devoid of housekeeping genes) in mouse fetal liver stem cells has been reported.18 The GenBank accession number of all 161 entries in the “transcription factor” category of this database were selected and used to identify the corresponding murine UniGene cluster for each entry (build version 129); the UniGene annotation was used to identify the human homologue, if available. All human genes that were also present in the CD34+ transcriptosome database were then selected for inclusion in the present study and updated to their corresponding entry in build version 135 of UniGene. GenBank and TIGR homology screens were performed as described above.

Selection of genes from the human CD34+transcriptosome database

The 15 970 genes in the human CD34+ transcriptosome database were searched for cDNAs that encode known TFs, and for those containing motifs that are frequently found in TFs and their interacting proteins. The analysis was based on a text search of the UniGene descriptor of the clones in the CD34+ database, rather than a direct homology search of the clone sequence. UniGene is a database that automatically collects and partitions GenBank and expressed sequence tag (EST) sequences into a nonredundant set of gene-oriented clusters by establishing sequence overlaps; each cluster represents a single potential transcript. Each cluster is annotated with a descriptor of the transcript that is the result of automated searches for sequence homologies to proteins from 8 organisms, using both nucleotide and protein sequence alignment; thus, a fair amount of functional prediction is available for each gene cluster even if it represents an EST sequence that has not been further studied. Each cluster is assigned a chromosomal location, based on sequence alignment. Details of the construction and updating of the UniGene database are available athttp://www.ncbi.nlm.nih.gov/UniGene/.

The UniGene cluster descriptors contained in the CD34+ transcriptosome database were searched for terms that are thought likely to annotate TFs, corepressors or coactivators, nuclear factors, and other DNA-interacting proteins. The resulting genes were updated, corrected for redundancy, and verified through homology screens. The database was visually inspected, and an additional 6 genes of known function, which clearly did not contain transcriptional regulatory activity, were removed from the database. A total of 285 genes resulted. Table1 presents these genes, categorized according to their function or functional motifs, with their UniGene number, chromosomal location, and UniGene descriptor. The cDNAs in each category are presented in the order from highest abundance to lowest, based on the measured level of expression in CD34+ cells, as reported in the database.17 

Table 1.

Potential human transcriptional regulators selected from the human CD34+ transcriptosome database

UniGene cluster IDGene nameGene descriptionBandFBAbundanceCharacterization
Transcription       
 Hs.321677 STAT3 Signal transducer and activator of transcription 3 (acute-phase response factor) 17q21 437.5 VH W 
 Hs.78881 MEF2B MADS box transcription enhancer factor 2, polypeptide B (myocyte enhancer factor 2B) 19p12 432.8 VH W 
 Hs.96055 E2F1 E2F transcription factor 1 20q11.2 224.9 VH W 
 *Hs.192861 SPIB Spi-B transcription factor (Spi-1/PU.1 related) 19q13.3-q13.4 207.0 VH W 
 Hs.22302 GTF3C4 General transcription factor IIIC, polypeptide 4 (90 kd) 9 200.8 VH W 
 Hs.74861 PC4 Activated RNA polymerase II transcription cofactor 4 8 151.9 VH W 
 Hs.3005 TFAP4 Transcription factor AP-4 (activating enhancer-binding protein 4) 16p13 146.9 VH W 
 Hs.79353 TFDP1 Transcription factor Dp-1 13q34 144.2 VH W  
 Hs.2815 POU6F1 POU domain, class 6, transcription factor 1 12 138.6 VH PC 
 Hs.19131 TFDP2 Transcription factor Dp-2 (E2F dimerization partner 2) 3q23 118.5 VH W  
 Hs.158195 HSF2 Heat shock transcription factor 2 6pter-p25.1 110.9 VH W 
 Hs.239720 CNOT2 CCR4-NOT transcription complex, subunit 2 12 99.4 H PC  
 Hs.93748  Homo sapiens clone moderately similar to transcription factor BTF3 N/A 81.7 H N  
 Hs.110103 RRN3 RNA polymerase I transcription factor RRN3 16p12 68.9 H W 
 Hs.334334 TFAP2A Transcription factor AP-2 α (activating enhancer-binding protein 2 alpha) 6p24 63.8 H W 
 Hs.80598 TCEA2 Transcription elongation factor A (SII), 2 N/A 59.4 H W  
 Hs.108106 ICBP90 Transcription factor 19p13.3 54.0 H PC 
 Hs.154970 TFCP2 Transcription factor CP2 12q13 48.0 H W  
 Hs.294101 PBX3 Pre–B-cell leukemia transcription factor 3 9q33-q34 43.1 H PC 
 *Hs.274184 TFE3 Transcription factor binding to IGHM enhancer 3 Xp11.22 40.9 H W 
 Hs.108371 E2F4 E2F transcription factor 4, p107/p130-binding 16q21-q22 40.4 H W 
 Hs.95243 TCEAL1 Transcription elongation factor A (SII)-like 1 Xq22.1 38.8 H W 
 Hs.1706 ISGF3G Interferon-stimulated transcription factor 3, γ (48 kd) 14q11.2 37.9 H W 
 Hs.9754 ATF5 Activating transcription factor 5 19q13.3 34.6 H W  
 Hs.244613 STAT5B Signal transducer and activator of transcription 5B 17q11.2 33.6 H W 
 Hs.169294 TCF7 Transcription factor 7 (T-cell specific, HMG-box) 5q31.1 31.7 H W 
 Hs.249184 TCF19 Transcription factor 19 (SC1) 6p21.3 29.5 H PC 
 Hs.7647 MAZ MYC-associated zinc finger protein (purine-binding transcription factor) 16p11.2 27.3 H W 
 Hs.29417 ZF HCF-binding transcription factor Zhangfei 11q14 24.0 I PC 
 Hs.155313 DATF1 Death-associated transcription factor 1 20 22.3 I PC  
 Hs.182280 MEF2A MADS box transcription enhancer factor 2, polypeptide A (myocyte enhancer factor 2A) 15q26 21.5 I W  
 Hs.26703 CNOT8 CCR4-NOT transcription complex, subunit 8 5q31-q33 21.4 I PC 
 Hs.279818 AF093680 Similar to mouse Glt3 or D malanogaster transcription factor IIB 16q13-q21 21.3 I W  
 Hs.1189 E2F3 E2F transcription factor 3 6p22 21.0 I W 
 Hs.68257 GTF2F1 General transcription factor IIF, polypeptide 1 (74-kD subunit) 19p13.3 19.0 I W 
 Hs.197540 HIF1A Hypoxia-inducible factor 1, α subunit (basic helix-loop-helix transcription factor) 14q21-q24 16.4 I W 
 *Hs.211588 POU4F1 POU domain, class 4, transcription factor 1 13q21.1-q22 15.9 I W 
 *Hs.155321 SRF Serum response factor (c-fos serum response element-binding transcription factor) 6pter-p24.1 15.1 I W 
 Hs.103989 NCYM DNA-binding transcriptional activator 2p24.1 14.9 I W 
 Hs.326198 TCF4 Transcription factor 4 18q21.1 14.7 I W 
 Hs.75133 TCF6L1 Transcription factor 6–like 1 (mitochondrial transcription
factor 1–like) 		7pter-cen 14.2 I W 
 Hs.101025 BTF3 Basic transcription factor 3 5 14.1 I W  
 Hs.166096 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial specific) 1q32.2 13.8 I W  
 Hs.797 NFYA Nuclear transcription factor Y, α 6p21.3 13.7 I W 
 Hs.129914 RUNX1 Runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 21q22.3 13.6 I W 
 Hs.247433 ATF6 Activating transcription factor 6 1q22-q23 13.5 I W  
 Hs.90304 GTF2H3 General transcription factor IIH, polypeptide 3 (34-kd subunit) 12 11.9 I W 
 Hs.78061 TCF21 Transcription factor 21 6pter-qter 11.1 I PC  
 Hs.75113 GTF3A General transcription factor IIIA 13q12.3-q13.1 10.0 I W 
 Hs.93728 PBX2 Pre–B-cell leukemia transcription factor 2 6p21.3 9.8 L W 
 Hs.16697 DR1 Down-regulator of transcription 1, TBP-binding (negative cofactor 2) 1p22.1 9.8 L W 
 Hs.182237 POU2F1 POU domain, class 2, transcription factor 1 1q22-q23 9.7 L W  
 Hs.765 GATA1 GATA-binding protein 1 (globin transcription factor 1) Xp11.23 9.0 L W 
 Hs.101842 ATBF1 AT-binding transcription factor 1 16q22.3-q23.1 8.7 L W 
 Hs.211581 MTF1 Metal-regulatory transcription factor 1 1p33 8.2 L W  
 Hs.173854 PAXIP1L PAX transcription activation domain interacting protein 1 like 7q36 8.2 L N  
 Hs.197764 TITF1 Thyroid transcription factor 1 14q13 8.0 L W 
 Hs.2982 SP4 Sp4 transcription factor 7p15 7.6 L W  
 Hs.59506 DMRT2 Doublesex and mab-3–related transcription factor 2 9p24.3 7.0 L PC 
 Hs.21486 STAT1 Signal transducer and activator of transcription 1, 91 kd 2q32.2 6.9 L W 
 Hs.278589 GTF2I General transcription factor II, i 7q11.23 6.6 L W  
 Hs.121895 RUNX2 Runt-related transcription factor 2 6p21 6.6 L W 
 Hs.460 ATF3 Activating transcription factor 3 1 6.3 L W  
 Hs.268115  ESTs, weakly similar toT08599 probable transcription factor CA150 [H sapiens] N/A 6.3 L N 
 Hs.171626 TCEB1L Transcription elongation factor B (SIII), polypeptide 1–like 5q31 6.1 L W 
 *Hs.1101 POU2F2 POU domain, class 2, transcription factor 2 19 6.1 L W 
 Hs.54780 TTF1 Transcription termination factor, RNA polymerase I 9 5.9 L W 
 *Hs.89781 UBTF Upstream binding transcription factor, RNA polymerase I 17q21.3 5.8 L W 
 *Hs.14963 FACTP140 Chromatin-specific transcription elongation factor, 140-kd subunit 14 5.8 L W 
 Hs.198166 ATF2 Activating transcription factor 2 2q32 5.7 L W  
 Hs.30824 LZTFL1 Leucine zipper transcription factor–like 1 3p21.3 5.5 L N 
 Hs.108300 CNOT3 CCR4-NOT transcription complex, subunit 3 19q13.4 5.3 L W 
 Hs.166017 MITF Microphthalmia-associated transcription factor 3p14.1-p12.3 5.0 L W 
 Hs.181243 ATF4 Activating transcription factor 4 (tax-responsive enhancer element B67) 22q13.1 4.9 L W 
 Hs.2331 E2F5 E2F transcription factor 5, p130-binding 8p22 4.9 L W 
 Hs.173638 TCF7L2 Transcription factor 7–like 2 (T-cell specific, HMG-box) 10q25.3 4.9 L W 
 Hs.24572  ESTs, weakly similar to TC17_human transcription
factor 17 [H sapiens] 		N/A 4.8 L N 
 Hs.191356 GTF2H2 General transcription factor IIH, polypeptide 2 (44-kd subunit) 5q12.2-q13.3 4.6 L W 
 *Hs.78869 TCEA1 Transcription elongation factor A (SII), 1 3p22-p21.3 4.6 L W 
 Hs.170019 RUNX3 Runt-related transcription factor 3 1p36 4.4 L W  
 Hs.154276 BACH1 BTB and CNC homology 1, basic leucine zipper transcription factor 1 21q22.11 4.4 L W  
 Hs.184771 NFIC Nuclear factor I/C (CCAAT-binding transcription factor) 19p13.3 4.4 L W  
 Hs.89578 GTF2H1 General transcription factor IIH, polypeptide 1 (62-kd subunit) 11p15.1-p14 4.3 L W 
 Hs.227630 REST RE1-silencing transcription factor 4q12-q13.3 4.3 L W 
 Hs.21704 TCF12 Transcription factor 12 (HTF4,helix-loop-helix transcription factors 4) 15q21 4.3 L PC 
 Hs.226318 CNOT7 CCR4-NOT transcription complex, subunit 7 8p22-p21.3 4.1 L PC 
 *Hs.13063 CA150 Transcription factor CA150 5q31 4.1 L W  
 Hs.150557 BTEB1 Basic transcription element binding protein 1 9q13 4.1 L W 
 Hs.84928 NFYB Nuclear transcription factor Y, β 12q22-q23 4.1 L W  
 Hs.35841 NFIX Nuclear factor I/X (CCAAT-binding transcription factor) 19p13.3 4.0 L PC 
 Hs.151139 ELF4 E74-like factor 4 (ets domain transcription factor) Xq26 3.9 L W  
 Hs.78995 MEF2C MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C) 5q14 3.9 L W  
 Hs.97996 MTERF Transcription termination factor, mitochondrial 7q21-q22 3.9 L W 
 Hs.119018 NRF Transcription factorNRF Xp21.1-q25 3.8 L W 
 Hs.100932 TCF17 Transcription factor 17 5q35.3 3.5 L PC  
 Hs.92282 PITX2 Pairedlike homeodomain transcription factor 2 4q25-q27 3.4 L PC 
 Hs.169853 TCF2 Transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor 17cen-q21.3 3.4 L W 
 Hs.181015 STAT6 Signal transducer and activator of transcription 6, interleukin-4 induced 12q13 3.3 L W 
 Hs.97624 HSF2BP Heat shock transcription factor 2 binding protein 21q22.3 3.2 L PC 
 Hs.171185 P38IP Transcription factor (p38 interacting protein) 13q12.213q14.2 3.2 L N 
 Hs.184693 TCEB1 Transcription elongation factor B (SIII), polypeptide 1 (15 kd, elongin C) 8 3.1 L W 
 Hs.20423 CNOT4 CCR4-NOT transcription complex, subunit 4 7q22-qter 3.1 L PC  
 Hs.76362 GTF2A2 General transcription factor IIA, 2 (12-kd subunit) 15q11.2 3.1 L W 
 *Hs.2430 TCFL1 Transcription factor–like 1 1q21 3.0 L PC  
 Hs.166 SREBF1 Sterol regulatory element binding transcription factor 1 17p11.2 3.0 L W 
Zinc       
 *Hs.194688 BAZ1B Bromodomain adjacent to zinc finger domain, 1B 7q11.23 439.3 VH PC 
 Hs.150390 ZNF262 Zinc finger protein 262 1p32-p34 369.5 VH N  
 Hs.1148 ZFP Zinc finger protein 3p22.3-p21.1 244.4 VH N 
 Hs.301637 ZNF258 Zinc finger protein 258 14q12 231.9 VH N  
 Hs.6557 ZNF161 Zinc finger protein 161 3q26.2 139.7 VH PC 
 Hs.108139 ZNF212 Zinc finger protein 212 7q36.1 118.5 VH N  
 Hs.169832 ZNF42 Zinc finger protein 42 (myeloid-specific retinoic acid–responsive) 19q13.2-q13.4 117.3 VH W 
 Hs.277401 BAZ2A Bromodomain adjacent to zinc finger domain, 2A 12q24.3-qter 108.3 VH N 
 Hs.151689 ZNF137 Zinc finger protein 137 (clone pHZ-30) 19q13.4 107.3 VH N  
 Hs.96448 ZNF193 Zinc finger protein 193 6p21.3 105.2 VH N 
 *Hs.58167 ZNF282 Zinc finger protein 282 7q35-q36 98.4 H PC  
 Hs.3057 ZNF74 Zinc finger protein 74 (Cos52) 22q11.21 88.8 H PC 
 Hs.70617 ZNF33A Zinc finger protein 33a (KOX 31) 10p11.2 78.6 H N 
 Hs.165983 FLJ22504 Hypothetical C2H2 zinc finger protein FLJ22504 20q11.21q13.12 62.6 H N 
 Hs.27801 ZNF278 Zinc finger protein 278 22q12.2 57.8 H W  
 Hs.194718 ZNF265 Zinc finger protein 265 1p31 57.2 H PC 
 Hs.142634 AF020591 Zinc finger protein 19 50.6 H N  
 Hs.183593 ZNF24 Zinc finger protein 24 (KOX 17) 18q12 46.1 H PC 
 Hs.180677 ZNF162 Zinc finger protein 162 11q13 46.0 H W  
 Hs.288773 ZNF294 Zinc finger protein 294 21q22.11 40.8 H N 
 Hs.22879 LOC51193 Zinc finger protein ANC_2H01 3q25.1-q25.33 39.5 H N 
 Hs.13128 ZNF205 Zinc finger protein 205 16p13.3 35.9 H N  
 Hs.182528 ZNF263 Zinc finger protein 263 16 35.4 H PC 
 Hs.119014 ZNF175 Zinc finger protein 175 19q13.4 29.9 H N  
 Hs.117077 ZNF264 Zinc finger protein 264 19q13.4 27.4 H N 
 *Hs.82210 ZNF220 Zinc finger protein 220 8p11 24.5 I PC  
 Hs.12940 ZHX1 Zinc-fingers and homeoboxes 1 8q 24.0 I PC 
 Hs.8383 BAZ2B Bromodomain adjacent to zinc finger domain, 2B 2q23-q24 22.5 I N  
 Hs.288658 ZNF35 Zinc finger protein 35 (clone HF.10) 3p22-p21 22.1 I PC 
 Hs.132390 ZNF36 Zinc finger protein 36 (KOX 18) 7q21.3-q22.1 21.4 I N 
 Hs.7137 LOC57862 Clones 23667 and 23775 zinc finger protein 14q24.3 20.3 I N  
 Hs.110839 ZFP95 Zinc finger protein homologous to Zfp95 in mouse 7q22 15.5 I N 
 Hs.10590 ZNF313 Zinc finger protein 313 20q11.21q11.23 15.1 I N  
 Hs.86356  EST, weakly similar to Z117_human zinc finger
protein 117 [H sapiens] 		N/A 14.3 I N 
 Hs.48589 ZNF228 Zinc finger protein 228 19q13.2 14.1 I N  
 Hs.50216 ZFD25 Zinc finger protein (ZFD25) 7q11.2 12.5 I N 
 Hs.301819 ZNF146 Zinc finger protein 146 19q13.1 10.9 I PC  
 Hs.74107 ZNF43 Zinc finger protein 43 (HTF6) 19p13.1-p12 10.6 I PC 
 Hs.33532 ZNF151 Zinc finger protein 151(pHZ-67) 1p36.2-p36.1 10.4 I W 
 Hs.20047 ZNFN2A1 Zinc finger protein, subfamily 2A (FYVE domain containing), 1 14q22-q24 10.4 I N 
 Hs.289104 ABP/ZF Alu-binding protein with zinc finger domain 7 10.3 I N  
 Hs.57419 CTCF CCCTC-binding factor (zinc finger protein) 16q21-q22.3 9.9 L W 
 *Hs.2110 ZNF9 Zinc finger protein 9 (a cellular retroviral nucleic acid binding protein) 3q13.3-q24 9.8 L PC  
 Hs.93005 SLUG Slug (chicken homolog), zinc finger protein 8q11 9.8 L W 
 *Hs.158174 ZNF184 Zinc finger protein 184 (Kruppel-like) 6p21.3 9.8 L N 
 Hs.59757 ZNF281 Zinc finger protein 281 1q32.1 9.7 L PC 
 *Hs.15220 ZFP106 Zinc finger protein 106 15 9.6 L N  
 Hs.237786 ZNF187 Zinc finger protein 187 6p22 8.9 L PC  
 Hs.62112 ZNF207 Zinc finger protein 207 17 8.8 L N 
 Hs.270435 FLJ12985 Hypothetical protein FLJ12985, human zinc finger
protein 91 		19q12 8.7 L N 
 Hs.89732 ZNF273 Zinc finger protein 273 N/A 8.4 L N  
 Hs.29159 ZNF75 Zinc finger protein 75 (D8C6) Xq26 8.0 L N 
 Hs.24125 LOC51780 Putative zinc finger protein 5q31 7.8 L PC 
 Hs.301059 FLJ12488 Hypothetical protein FLJ12488, moderately human zinc
finger protein 93 		N/A 7.5 L N  
 Hs.19585 SZF1 KRAB-zinc finger protein SZF1-1 3p21 7.2 L PC 
 Hs.154095 ZNF143 Zinc finger protein 143 (clone pHZ-1) 11p15.4 7.1 L PC 
 *Hs.30503  H sapiens cDNA FLJ11344 fis, clone PLACE1010870, moderately similar to zinc finger protein 91 N/A 7.0 L N 
 Hs.9786 ZNF275 Zinc finger protein 275 N/A 6.7 L N  
 Hs.3053 ZID Zinc finger protein with interaction domain 9q33.1-q33.3 6.3 L PC 
 Hs.20631 PEGASUS Zinc finger protein, subfamily 1A, 5 (Pegasus) 10q26 6.0 L PC  
 Hs.20082 ZNF3 Zinc finger protein 3 (A8-51) 5 5.9 L N 
 *Hs.108642 ZNF22 Zinc finger protein 22(KOX 15) 10q11 5.5 L N 
 Hs.78743 ZNF131 Zinc finger protein 131 (clone pHZ-10) 5p12-p11 5.5 L N  
 Hs.29222 ZNF76 Zinc finger protein 76 (expressed in testis) 6p21.3-p21.2 5.4 L PC 
 *Hs.287331 ZNF286 Zinc finger proteinZNF286 17p11.2 5.3 L N 
 *Hs.69997 ZNF238 Zinc finger protein 238 1q44-qter 5.3 L PC  
 Hs.109526 ZNF198 Zinc finger protein 198 13q11-q12 5.3 L PC 
 Hs.85505  ESTs, weakly similar toZF37_human zinc finger
proteinZFP-37 [H sapiens] 		N/A 5.3 L N  
 Hs.48029 SNAI1 Snail 1 (Drosophila homolog), zinc finger protein 20q13.1-q13.2 5.1 L PC 
 Hs.172979 ZNF177 Zinc finger protein 177 19pter-19p13.3 4.8 L PC 
 Hs.155204 ZNF174 Zinc finger protein 174 16p13.3 4.8 L PC  
 Hs.86371 ZNF254 Zinc finger protein 254 19p13.12-p13.11 4.8 L N 
 Hs.180248 ZNF124 Zinc finger protein 124(HZF-16) 1q44 4.6 L PC 
 Hs.279914 ZNF232 Zinc finger protein 232 17p13-p12 4.6 L PC  
 Hs.15110 ZNF211 Zinc finger protein 211 19q13.4 4.3 L N 
 Hs.55481 ZNF165 Zinc finger protein 165 6p21.3 4.3 L N  
 Hs.33268  H sapiens weakly similar to zinc finger protein 84 N/A 4.2 L N  
 Hs.197219 ZNF14 Zinc finger protein 14 (KOX 6) 19p13.3-p13.2 4.2 L N 
 Hs.296365 ZF5128 Zinc finger protein 19 4.1 L N 
 Hs.22182 ZNF23 Zinc finger protein 23 (KOX 16) 16q22 4.1 L N  
 Hs.183291 ZNF268 Zinc finger protein 268 5 4.0 L N 
 Hs.156000 ZFP161 Zinc finger protein homologous toZfp161 in mouse 18pter-p11.2 4.0 L N 
 Hs.72318  H sapiens moderately similar to zinc finger protein 91 N/A 4.0 L N 
 Hs.64794 ZNF183 Zinc finger protein 183 (RING finger, C3HC4 type) Xq25-q26 4.0 L N 
 *Hs.110956 ZNF20 Zinc finger protein 20(KOX 13) 19p13.3-p13.2 4.0 L PC 
 Hs.184669 ZNF144 Zinc finger protein 144(Mel-18) 17 3.7 L W 
 Hs.23476 CIZ1 Cip1-interacting zinc finger protein 9q34.1 3.4 L PC  
 Hs.31324 ZNF155 Zinc finger protein 155(pHZ-96) 19q13.2-q13.32 3.2 L N 
 Hs.23019 ZNF16 Zinc finger protein 16 (KOX 9) 8q24 3.1 L N  
 Hs.88219 ZNF200 Zinc finger protein 200 16p13.3 3.1 L N 
Activator       
 Hs.146847 TANK TRAF family member-associated NFKB activator 2q24-q31 84.0 H W 
 Hs.40403 CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 Xq13.1 37.8 H W 
 Hs.198468 PPARGC1 Peroxisome proliferative activated receptor, γ, coactivator 1 4p15.1 13.7 I W 
 Hs.82071 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 6q23.3 12.3 I W 
 Hs.3076 MHC2TA MHC class II transactivator 16p13 10.0 I W 
 Hs.283689 ACT Activator of CREM in testis 6q16.1-q16.3 3.9 L W 
 Hs.79093 p100 EBNA-2 coactivator (100 kd) 7q31.3 3.0 L PC 
Enhancer       
 Hs.83958 TLE4 Transducinlike enhancer of split 4, homolog of DrosophilaE(sp1) 9 721.5 VH W  
 Hs.226573 IKBKB Inhibitor of κ light polypeptide gene enhancer in B-cells, kinase β 8p11.2 106.5 VH W 
 Hs.28935 TLE1 Transducinlike enhancer of split 1, homolog of Drosophila E(sp1) 19p13.3 58.4 H W 
 *Hs.75117 ILF2 Interleukin enhancer binding factor 2, 45 kd N/A 52.4 H W 
 Hs.234434 HEY1 Hairy/enhancer-of-split related with YRPW motif 1 8q21 29.9 H PC  
 Hs.81328 NFKBIA Nuclear factor of κ light polypeptide gene enhancer in B cells inhibitor, α 14q13 23.2 I W 
 Hs.332173 TLE2 Transducinlike enhancer of split 2, homolog of Drosophila E(sp1) 19p13.3 18.8 I W 
 Hs.99029 CEBPB CCAAT/enhancer binding protein(C/EBP), β 20q13.1 11.1 I W 
 Hs.256583 ILF3 Interleukin enhancer binding factor 3, 90 kd 19p13 10.0 I PC 
 *Hs.83428 NFKB1 Nuclear factor of κ light polypeptide gene enhancer in B cells 1 (p105) 4q24 9.7 L W 
 Hs.2227 CEBPG CCAAT/enhancer binding protein (C/EBP), γ 19 5.9 L W  
 Hs.9731 NFKBIB Nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor, β 19q13.1 4.6 L W  
 Hs.306 HIVEP1 Human immunodeficiency virus type I enhancer-binding protein 1 6p24-p22.3 3.8 L W 
 Hs.76722 CEBPD CCAAT/enhancer binding protein(C/EBP), δ 8p11.2-p11.1 3.8 L W 
Forkhead       
 Hs.44481 FOXF2 Forkhead box F2 6p25.3 151.3 VH PC 
 Hs.2714 FOXG1B Forkhead box G1B 14q12-q13 67.9 H W  
 Hs.56213  ESTs, highly similar to FXD3_human forkhead box
protein D3 [H sapiens] 		N/A 55.0 H N 
 Hs.239 FOXM1 Forkhead box M1 12p13 25.9 H W 
 Hs.155591 FOXF1 Forkhead box F1 16q24 21.8 I PC 
 Hs.112968 FOXE3 Forkhead box E3 1p32 7.9 L PC 
 Hs.284186 FOXC1 Forkhead box C1 6p25 6.3 L PC 
 *Hs.170133 FOXO1A Forkhead box O1A (rhabdomyosarcoma) 13q14.1 5.7 L PC 
 Hs.96028 FOXD1 Forkhead box D1 5q12-q13 4.5 L PC 
 Hs.120844 LOC55810 FOXJ2 forkhead factor 12pter-p13.31 4.1 L PC 
 Hs.93974 FOXJ1 Forkhead box J1 17q22-17q25 3.3 L PC 
Helix       
 Hs.76884 ID3 Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 1p36.13-p36.12 30.8 H W 
 Hs.198998 CHUK Conserved helix-loop-helix ubiquitous kinase 10q24-q25 10 I W  
 Hs.30956 NHLH1 Nescient helix loop helix 1 1q22 8.2 L W 
 *Hs.34853 ID4 Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 6p22-p21 3.7 L W 
 Hs.46296 NHLH2 Nescient helix loop helix 2 1p12-p11 3.6 L PC  
 Hs.75424 ID1 Inhibitor of DNA binding 1, dominant negative helix-loop-helix protein 20q11 3.3 L W 
Homeobox       
 Hs.55967 SHOX2 Sort stature homeobox 2 3q25-q26.1 220.3 VH PC 
 Hs.125231 HPX42B Hemopoietic progenitor homeobox 10q26 6.3 L PC 
 *Hs.90077 TGIF TG-interacting factor (TALE family homeobox) 18p11.3 4.9 L W 
Leucine       
 Hs.158205 BLZF1 Basic leucine zipper nuclear factor 1(JEM-1) 1q24 3.4 L PC 
Non-POU       
 Hs.172207 NONO Non-POU domain-containing, octamer-binding Xq13.1 19.5 I W 
Nuclear       
 Hs.249247 FBRNP Heterogeneous nuclear protein similar to rat helix destabilizing protein 10 31.4 H PC 
Oncogene       
 Hs.858 RELB v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of κ light polypeptide gene enhancer in B-cells 3) 19q13.2 260.5 VH W  
 Hs.75569 RELA v-rel avian reticuloendotheliosis viral oncogene homolog A (nuclear factor of κ light polypeptide gene enhancer in B-cells 3 [p65]) 11q13 143.6 VH W  
 Hs.198951 JUNB jun B proto-oncogene 19p13.2 56.9 H W 
 Hs.78465 JUN v-jun avian sarcoma virus 17 oncogene homolog 1p32-p31 47.2 H W  
 Hs.300592 MYBL1 v-myb avian myeloblastosis viral oncogene homolog–like 1 8q22 43.0 H W  
 Hs.51305 MAFF v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein F 22q13.1 36.4 H PC  
 Hs.2780 JUND jun D proto-oncogene 19p13.2 20.8 I W 
 *Hs.79070 MYC v-myc avian myelocytomatosis viral oncogene homolog 8q24.12-q24.13 18.3 I W 
 Hs.85146 ETS2 v-ets avian erythroblastosis virus E26 oncogene homolog 2 21q22.2 11.0 I W 
 Hs.179718 MYBL2 v-myb avian myeloblastosis viral oncogene homolog–like 2 20q13.1 9.5 L W 
 Hs.92137 MYCL1 v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived 1p34.3 8.1 L W 
 Hs.724 THRA Thyroid hormone receptor, α (avian erythroblastic leukemia viral [v-erb-a] oncogene homolog) 17q11.2 6.2 L W  
 Hs.2969 SKI v-ski avian sarcoma viral oncogene homolog 1q22-q24 5.3 L W 
 Hs.110713 DEK DEK oncogene (DNA binding) 6p23 4.9 L W 
 *Hs.157441 SPI1 Spleen focus-forming virus (SFFV) proviral integration oncogene spi1 11p11.2 4.5 L W 
 Hs.181128 ELK1 ELK1, member of ETS oncogene family Xp11.2 4.4 L W  
 Hs.431 BMI1 Murine leukemia viral (bmi-1) oncogene homolog 10p13 4.0 L W 
 Hs.1334 MYB v-myb avian myeloblastosis viral oncogene homolog 6q22-q23 3.7 L W  
 Hs.252229 MAFG v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein G 17q25 3.5 L W  
 Hs.30250 MAF v-maf musculoaponeurotic fibrosarcoma (avian) oncogene homolog 16q22-q23 3.1 L W 
PHD       
 Hs.166204 PHF1 PHD finger protein 1 6p21.3 7.2 L PC 
Repressor       
 Hs.144904 NCOR1 Nuclear receptor corepressor 1 17p11.2 21.2 I W 
 Hs.89421 CIR CBF1 interacting corepressor 2p23.3-q24.3 6.7 L W 
 Hs.7222 RBAK RB-associated KRAB repressor 7 6.0 L PC  
 Hs.5710 CREG Cellular repressor of E1A-stimulated genes 1q24 5.1 L PC 
 Hs.287994 NCOR2 Nuclear receptor corepressor 2 12q24 3.7 L W 
Ring       
 *Hs.14084 RNF7 Ring finger protein 7 3q22-q24 401.9 VH PC 
 Hs.216354 RNF5 Ring finger protein 5 6p21.3 396.4 VH N  
 Hs.97176 RNF25 Ring finger protein 25 2p23.3-q34 358.7 VH N 
 Hs.59545 RNF15 Ring finger protein 15 6p21.3 220.9 VH N  
 Hs.8834 RNF3 Ring finger protein 3 4p16.3 58.4 H N 
 Hs.23794 CHFR Checkpoint with forkhead and ring finger domains 12 42.1 H PC  
 Hs.32597 RNF6 Ring finger protein (C3H2C3 type) 6 13q12.2 31.5 H N 
 *Hs.6900 RNF13 Ring finger protein 13 3p13-q26.1 10.4 I N  
 Hs.61515  H sapiens, similar to ring finger protein 23, clone MGC:2475, mRNA, complete cds N/A 6.4 L N  
 Hs.7838 MKRN1 Makorin, ring finger protein, 1 7q34 5.9 L PC 
 Hs.35384 RING1 Ring finger protein 1 6p21.3 4.4 L W  
 Hs.274295 RNF9 Ring finger protein 9 6p21.3 4.3 L PC  
 Hs.59106 CGR19 Cell growth regulatory with ring finger domain 14q21.1-q23.3 4.2 L N  
 Hs.91096 RNF Ring finger protein 6p21.3 4.0 L N 
Others       
 Hs.326876 SOX6 H sapiens SOX6 mRNA, complete cds 11p15.3 98.2 H W 
 Hs.185708 EBF Early B-cell factor 5q34 81.8 H W 
 Hs.288697 MGC11349 Hypothetical protein MGC11349 3p13-q26.1 12.2 I N  
 Hs.23240  H sapiens cDNA: FLJ21848 fis, clone HEP01925 N/A 11.6 I N  
 Hs.278270 P23 Unactive progesterone receptor, 23 kD 12 5.7 L PC 
 Hs.7367  H sapiens BTB domain protein (BDPL) mRNA, partial cds N/A 4.3 L PC 
UniGene cluster IDGene nameGene descriptionBandFBAbundanceCharacterization
Transcription       
 Hs.321677 STAT3 Signal transducer and activator of transcription 3 (acute-phase response factor) 17q21 437.5 VH W 
 Hs.78881 MEF2B MADS box transcription enhancer factor 2, polypeptide B (myocyte enhancer factor 2B) 19p12 432.8 VH W 
 Hs.96055 E2F1 E2F transcription factor 1 20q11.2 224.9 VH W 
 *Hs.192861 SPIB Spi-B transcription factor (Spi-1/PU.1 related) 19q13.3-q13.4 207.0 VH W 
 Hs.22302 GTF3C4 General transcription factor IIIC, polypeptide 4 (90 kd) 9 200.8 VH W 
 Hs.74861 PC4 Activated RNA polymerase II transcription cofactor 4 8 151.9 VH W 
 Hs.3005 TFAP4 Transcription factor AP-4 (activating enhancer-binding protein 4) 16p13 146.9 VH W 
 Hs.79353 TFDP1 Transcription factor Dp-1 13q34 144.2 VH W  
 Hs.2815 POU6F1 POU domain, class 6, transcription factor 1 12 138.6 VH PC 
 Hs.19131 TFDP2 Transcription factor Dp-2 (E2F dimerization partner 2) 3q23 118.5 VH W  
 Hs.158195 HSF2 Heat shock transcription factor 2 6pter-p25.1 110.9 VH W 
 Hs.239720 CNOT2 CCR4-NOT transcription complex, subunit 2 12 99.4 H PC  
 Hs.93748  Homo sapiens clone moderately similar to transcription factor BTF3 N/A 81.7 H N  
 Hs.110103 RRN3 RNA polymerase I transcription factor RRN3 16p12 68.9 H W 
 Hs.334334 TFAP2A Transcription factor AP-2 α (activating enhancer-binding protein 2 alpha) 6p24 63.8 H W 
 Hs.80598 TCEA2 Transcription elongation factor A (SII), 2 N/A 59.4 H W  
 Hs.108106 ICBP90 Transcription factor 19p13.3 54.0 H PC 
 Hs.154970 TFCP2 Transcription factor CP2 12q13 48.0 H W  
 Hs.294101 PBX3 Pre–B-cell leukemia transcription factor 3 9q33-q34 43.1 H PC 
 *Hs.274184 TFE3 Transcription factor binding to IGHM enhancer 3 Xp11.22 40.9 H W 
 Hs.108371 E2F4 E2F transcription factor 4, p107/p130-binding 16q21-q22 40.4 H W 
 Hs.95243 TCEAL1 Transcription elongation factor A (SII)-like 1 Xq22.1 38.8 H W 
 Hs.1706 ISGF3G Interferon-stimulated transcription factor 3, γ (48 kd) 14q11.2 37.9 H W 
 Hs.9754 ATF5 Activating transcription factor 5 19q13.3 34.6 H W  
 Hs.244613 STAT5B Signal transducer and activator of transcription 5B 17q11.2 33.6 H W 
 Hs.169294 TCF7 Transcription factor 7 (T-cell specific, HMG-box) 5q31.1 31.7 H W 
 Hs.249184 TCF19 Transcription factor 19 (SC1) 6p21.3 29.5 H PC 
 Hs.7647 MAZ MYC-associated zinc finger protein (purine-binding transcription factor) 16p11.2 27.3 H W 
 Hs.29417 ZF HCF-binding transcription factor Zhangfei 11q14 24.0 I PC 
 Hs.155313 DATF1 Death-associated transcription factor 1 20 22.3 I PC  
 Hs.182280 MEF2A MADS box transcription enhancer factor 2, polypeptide A (myocyte enhancer factor 2A) 15q26 21.5 I W  
 Hs.26703 CNOT8 CCR4-NOT transcription complex, subunit 8 5q31-q33 21.4 I PC 
 Hs.279818 AF093680 Similar to mouse Glt3 or D malanogaster transcription factor IIB 16q13-q21 21.3 I W  
 Hs.1189 E2F3 E2F transcription factor 3 6p22 21.0 I W 
 Hs.68257 GTF2F1 General transcription factor IIF, polypeptide 1 (74-kD subunit) 19p13.3 19.0 I W 
 Hs.197540 HIF1A Hypoxia-inducible factor 1, α subunit (basic helix-loop-helix transcription factor) 14q21-q24 16.4 I W 
 *Hs.211588 POU4F1 POU domain, class 4, transcription factor 1 13q21.1-q22 15.9 I W 
 *Hs.155321 SRF Serum response factor (c-fos serum response element-binding transcription factor) 6pter-p24.1 15.1 I W 
 Hs.103989 NCYM DNA-binding transcriptional activator 2p24.1 14.9 I W 
 Hs.326198 TCF4 Transcription factor 4 18q21.1 14.7 I W 
 Hs.75133 TCF6L1 Transcription factor 6–like 1 (mitochondrial transcription
factor 1–like) 		7pter-cen 14.2 I W 
 Hs.101025 BTF3 Basic transcription factor 3 5 14.1 I W  
 Hs.166096 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial specific) 1q32.2 13.8 I W  
 Hs.797 NFYA Nuclear transcription factor Y, α 6p21.3 13.7 I W 
 Hs.129914 RUNX1 Runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 21q22.3 13.6 I W 
 Hs.247433 ATF6 Activating transcription factor 6 1q22-q23 13.5 I W  
 Hs.90304 GTF2H3 General transcription factor IIH, polypeptide 3 (34-kd subunit) 12 11.9 I W 
 Hs.78061 TCF21 Transcription factor 21 6pter-qter 11.1 I PC  
 Hs.75113 GTF3A General transcription factor IIIA 13q12.3-q13.1 10.0 I W 
 Hs.93728 PBX2 Pre–B-cell leukemia transcription factor 2 6p21.3 9.8 L W 
 Hs.16697 DR1 Down-regulator of transcription 1, TBP-binding (negative cofactor 2) 1p22.1 9.8 L W 
 Hs.182237 POU2F1 POU domain, class 2, transcription factor 1 1q22-q23 9.7 L W  
 Hs.765 GATA1 GATA-binding protein 1 (globin transcription factor 1) Xp11.23 9.0 L W 
 Hs.101842 ATBF1 AT-binding transcription factor 1 16q22.3-q23.1 8.7 L W 
 Hs.211581 MTF1 Metal-regulatory transcription factor 1 1p33 8.2 L W  
 Hs.173854 PAXIP1L PAX transcription activation domain interacting protein 1 like 7q36 8.2 L N  
 Hs.197764 TITF1 Thyroid transcription factor 1 14q13 8.0 L W 
 Hs.2982 SP4 Sp4 transcription factor 7p15 7.6 L W  
 Hs.59506 DMRT2 Doublesex and mab-3–related transcription factor 2 9p24.3 7.0 L PC 
 Hs.21486 STAT1 Signal transducer and activator of transcription 1, 91 kd 2q32.2 6.9 L W 
 Hs.278589 GTF2I General transcription factor II, i 7q11.23 6.6 L W  
 Hs.121895 RUNX2 Runt-related transcription factor 2 6p21 6.6 L W 
 Hs.460 ATF3 Activating transcription factor 3 1 6.3 L W  
 Hs.268115  ESTs, weakly similar toT08599 probable transcription factor CA150 [H sapiens] N/A 6.3 L N 
 Hs.171626 TCEB1L Transcription elongation factor B (SIII), polypeptide 1–like 5q31 6.1 L W 
 *Hs.1101 POU2F2 POU domain, class 2, transcription factor 2 19 6.1 L W 
 Hs.54780 TTF1 Transcription termination factor, RNA polymerase I 9 5.9 L W 
 *Hs.89781 UBTF Upstream binding transcription factor, RNA polymerase I 17q21.3 5.8 L W 
 *Hs.14963 FACTP140 Chromatin-specific transcription elongation factor, 140-kd subunit 14 5.8 L W 
 Hs.198166 ATF2 Activating transcription factor 2 2q32 5.7 L W  
 Hs.30824 LZTFL1 Leucine zipper transcription factor–like 1 3p21.3 5.5 L N 
 Hs.108300 CNOT3 CCR4-NOT transcription complex, subunit 3 19q13.4 5.3 L W 
 Hs.166017 MITF Microphthalmia-associated transcription factor 3p14.1-p12.3 5.0 L W 
 Hs.181243 ATF4 Activating transcription factor 4 (tax-responsive enhancer element B67) 22q13.1 4.9 L W 
 Hs.2331 E2F5 E2F transcription factor 5, p130-binding 8p22 4.9 L W 
 Hs.173638 TCF7L2 Transcription factor 7–like 2 (T-cell specific, HMG-box) 10q25.3 4.9 L W 
 Hs.24572  ESTs, weakly similar to TC17_human transcription
factor 17 [H sapiens] 		N/A 4.8 L N 
 Hs.191356 GTF2H2 General transcription factor IIH, polypeptide 2 (44-kd subunit) 5q12.2-q13.3 4.6 L W 
 *Hs.78869 TCEA1 Transcription elongation factor A (SII), 1 3p22-p21.3 4.6 L W 
 Hs.170019 RUNX3 Runt-related transcription factor 3 1p36 4.4 L W  
 Hs.154276 BACH1 BTB and CNC homology 1, basic leucine zipper transcription factor 1 21q22.11 4.4 L W  
 Hs.184771 NFIC Nuclear factor I/C (CCAAT-binding transcription factor) 19p13.3 4.4 L W  
 Hs.89578 GTF2H1 General transcription factor IIH, polypeptide 1 (62-kd subunit) 11p15.1-p14 4.3 L W 
 Hs.227630 REST RE1-silencing transcription factor 4q12-q13.3 4.3 L W 
 Hs.21704 TCF12 Transcription factor 12 (HTF4,helix-loop-helix transcription factors 4) 15q21 4.3 L PC 
 Hs.226318 CNOT7 CCR4-NOT transcription complex, subunit 7 8p22-p21.3 4.1 L PC 
 *Hs.13063 CA150 Transcription factor CA150 5q31 4.1 L W  
 Hs.150557 BTEB1 Basic transcription element binding protein 1 9q13 4.1 L W 
 Hs.84928 NFYB Nuclear transcription factor Y, β 12q22-q23 4.1 L W  
 Hs.35841 NFIX Nuclear factor I/X (CCAAT-binding transcription factor) 19p13.3 4.0 L PC 
 Hs.151139 ELF4 E74-like factor 4 (ets domain transcription factor) Xq26 3.9 L W  
 Hs.78995 MEF2C MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C) 5q14 3.9 L W  
 Hs.97996 MTERF Transcription termination factor, mitochondrial 7q21-q22 3.9 L W 
 Hs.119018 NRF Transcription factorNRF Xp21.1-q25 3.8 L W 
 Hs.100932 TCF17 Transcription factor 17 5q35.3 3.5 L PC  
 Hs.92282 PITX2 Pairedlike homeodomain transcription factor 2 4q25-q27 3.4 L PC 
 Hs.169853 TCF2 Transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor 17cen-q21.3 3.4 L W 
 Hs.181015 STAT6 Signal transducer and activator of transcription 6, interleukin-4 induced 12q13 3.3 L W 
 Hs.97624 HSF2BP Heat shock transcription factor 2 binding protein 21q22.3 3.2 L PC 
 Hs.171185 P38IP Transcription factor (p38 interacting protein) 13q12.213q14.2 3.2 L N 
 Hs.184693 TCEB1 Transcription elongation factor B (SIII), polypeptide 1 (15 kd, elongin C) 8 3.1 L W 
 Hs.20423 CNOT4 CCR4-NOT transcription complex, subunit 4 7q22-qter 3.1 L PC  
 Hs.76362 GTF2A2 General transcription factor IIA, 2 (12-kd subunit) 15q11.2 3.1 L W 
 *Hs.2430 TCFL1 Transcription factor–like 1 1q21 3.0 L PC  
 Hs.166 SREBF1 Sterol regulatory element binding transcription factor 1 17p11.2 3.0 L W 
Zinc       
 *Hs.194688 BAZ1B Bromodomain adjacent to zinc finger domain, 1B 7q11.23 439.3 VH PC 
 Hs.150390 ZNF262 Zinc finger protein 262 1p32-p34 369.5 VH N  
 Hs.1148 ZFP Zinc finger protein 3p22.3-p21.1 244.4 VH N 
 Hs.301637 ZNF258 Zinc finger protein 258 14q12 231.9 VH N  
 Hs.6557 ZNF161 Zinc finger protein 161 3q26.2 139.7 VH PC 
 Hs.108139 ZNF212 Zinc finger protein 212 7q36.1 118.5 VH N  
 Hs.169832 ZNF42 Zinc finger protein 42 (myeloid-specific retinoic acid–responsive) 19q13.2-q13.4 117.3 VH W 
 Hs.277401 BAZ2A Bromodomain adjacent to zinc finger domain, 2A 12q24.3-qter 108.3 VH N 
 Hs.151689 ZNF137 Zinc finger protein 137 (clone pHZ-30) 19q13.4 107.3 VH N  
 Hs.96448 ZNF193 Zinc finger protein 193 6p21.3 105.2 VH N 
 *Hs.58167 ZNF282 Zinc finger protein 282 7q35-q36 98.4 H PC  
 Hs.3057 ZNF74 Zinc finger protein 74 (Cos52) 22q11.21 88.8 H PC 
 Hs.70617 ZNF33A Zinc finger protein 33a (KOX 31) 10p11.2 78.6 H N 
 Hs.165983 FLJ22504 Hypothetical C2H2 zinc finger protein FLJ22504 20q11.21q13.12 62.6 H N 
 Hs.27801 ZNF278 Zinc finger protein 278 22q12.2 57.8 H W  
 Hs.194718 ZNF265 Zinc finger protein 265 1p31 57.2 H PC 
 Hs.142634 AF020591 Zinc finger protein 19 50.6 H N  
 Hs.183593 ZNF24 Zinc finger protein 24 (KOX 17) 18q12 46.1 H PC 
 Hs.180677 ZNF162 Zinc finger protein 162 11q13 46.0 H W  
 Hs.288773 ZNF294 Zinc finger protein 294 21q22.11 40.8 H N 
 Hs.22879 LOC51193 Zinc finger protein ANC_2H01 3q25.1-q25.33 39.5 H N 
 Hs.13128 ZNF205 Zinc finger protein 205 16p13.3 35.9 H N  
 Hs.182528 ZNF263 Zinc finger protein 263 16 35.4 H PC 
 Hs.119014 ZNF175 Zinc finger protein 175 19q13.4 29.9 H N  
 Hs.117077 ZNF264 Zinc finger protein 264 19q13.4 27.4 H N 
 *Hs.82210 ZNF220 Zinc finger protein 220 8p11 24.5 I PC  
 Hs.12940 ZHX1 Zinc-fingers and homeoboxes 1 8q 24.0 I PC 
 Hs.8383 BAZ2B Bromodomain adjacent to zinc finger domain, 2B 2q23-q24 22.5 I N  
 Hs.288658 ZNF35 Zinc finger protein 35 (clone HF.10) 3p22-p21 22.1 I PC 
 Hs.132390 ZNF36 Zinc finger protein 36 (KOX 18) 7q21.3-q22.1 21.4 I N 
 Hs.7137 LOC57862 Clones 23667 and 23775 zinc finger protein 14q24.3 20.3 I N  
 Hs.110839 ZFP95 Zinc finger protein homologous to Zfp95 in mouse 7q22 15.5 I N 
 Hs.10590 ZNF313 Zinc finger protein 313 20q11.21q11.23 15.1 I N  
 Hs.86356  EST, weakly similar to Z117_human zinc finger
protein 117 [H sapiens] 		N/A 14.3 I N 
 Hs.48589 ZNF228 Zinc finger protein 228 19q13.2 14.1 I N  
 Hs.50216 ZFD25 Zinc finger protein (ZFD25) 7q11.2 12.5 I N 
 Hs.301819 ZNF146 Zinc finger protein 146 19q13.1 10.9 I PC  
 Hs.74107 ZNF43 Zinc finger protein 43 (HTF6) 19p13.1-p12 10.6 I PC 
 Hs.33532 ZNF151 Zinc finger protein 151(pHZ-67) 1p36.2-p36.1 10.4 I W 
 Hs.20047 ZNFN2A1 Zinc finger protein, subfamily 2A (FYVE domain containing), 1 14q22-q24 10.4 I N 
 Hs.289104 ABP/ZF Alu-binding protein with zinc finger domain 7 10.3 I N  
 Hs.57419 CTCF CCCTC-binding factor (zinc finger protein) 16q21-q22.3 9.9 L W 
 *Hs.2110 ZNF9 Zinc finger protein 9 (a cellular retroviral nucleic acid binding protein) 3q13.3-q24 9.8 L PC  
 Hs.93005 SLUG Slug (chicken homolog), zinc finger protein 8q11 9.8 L W 
 *Hs.158174 ZNF184 Zinc finger protein 184 (Kruppel-like) 6p21.3 9.8 L N 
 Hs.59757 ZNF281 Zinc finger protein 281 1q32.1 9.7 L PC 
 *Hs.15220 ZFP106 Zinc finger protein 106 15 9.6 L N  
 Hs.237786 ZNF187 Zinc finger protein 187 6p22 8.9 L PC  
 Hs.62112 ZNF207 Zinc finger protein 207 17 8.8 L N 
 Hs.270435 FLJ12985 Hypothetical protein FLJ12985, human zinc finger
protein 91 		19q12 8.7 L N 
 Hs.89732 ZNF273 Zinc finger protein 273 N/A 8.4 L N  
 Hs.29159 ZNF75 Zinc finger protein 75 (D8C6) Xq26 8.0 L N 
 Hs.24125 LOC51780 Putative zinc finger protein 5q31 7.8 L PC 
 Hs.301059 FLJ12488 Hypothetical protein FLJ12488, moderately human zinc
finger protein 93 		N/A 7.5 L N  
 Hs.19585 SZF1 KRAB-zinc finger protein SZF1-1 3p21 7.2 L PC 
 Hs.154095 ZNF143 Zinc finger protein 143 (clone pHZ-1) 11p15.4 7.1 L PC 
 *Hs.30503  H sapiens cDNA FLJ11344 fis, clone PLACE1010870, moderately similar to zinc finger protein 91 N/A 7.0 L N 
 Hs.9786 ZNF275 Zinc finger protein 275 N/A 6.7 L N  
 Hs.3053 ZID Zinc finger protein with interaction domain 9q33.1-q33.3 6.3 L PC 
 Hs.20631 PEGASUS Zinc finger protein, subfamily 1A, 5 (Pegasus) 10q26 6.0 L PC  
 Hs.20082 ZNF3 Zinc finger protein 3 (A8-51) 5 5.9 L N 
 *Hs.108642 ZNF22 Zinc finger protein 22(KOX 15) 10q11 5.5 L N 
 Hs.78743 ZNF131 Zinc finger protein 131 (clone pHZ-10) 5p12-p11 5.5 L N  
 Hs.29222 ZNF76 Zinc finger protein 76 (expressed in testis) 6p21.3-p21.2 5.4 L PC 
 *Hs.287331 ZNF286 Zinc finger proteinZNF286 17p11.2 5.3 L N 
 *Hs.69997 ZNF238 Zinc finger protein 238 1q44-qter 5.3 L PC  
 Hs.109526 ZNF198 Zinc finger protein 198 13q11-q12 5.3 L PC 
 Hs.85505  ESTs, weakly similar toZF37_human zinc finger
proteinZFP-37 [H sapiens] 		N/A 5.3 L N  
 Hs.48029 SNAI1 Snail 1 (Drosophila homolog), zinc finger protein 20q13.1-q13.2 5.1 L PC 
 Hs.172979 ZNF177 Zinc finger protein 177 19pter-19p13.3 4.8 L PC 
 Hs.155204 ZNF174 Zinc finger protein 174 16p13.3 4.8 L PC  
 Hs.86371 ZNF254 Zinc finger protein 254 19p13.12-p13.11 4.8 L N 
 Hs.180248 ZNF124 Zinc finger protein 124(HZF-16) 1q44 4.6 L PC 
 Hs.279914 ZNF232 Zinc finger protein 232 17p13-p12 4.6 L PC  
 Hs.15110 ZNF211 Zinc finger protein 211 19q13.4 4.3 L N 
 Hs.55481 ZNF165 Zinc finger protein 165 6p21.3 4.3 L N  
 Hs.33268  H sapiens weakly similar to zinc finger protein 84 N/A 4.2 L N  
 Hs.197219 ZNF14 Zinc finger protein 14 (KOX 6) 19p13.3-p13.2 4.2 L N 
 Hs.296365 ZF5128 Zinc finger protein 19 4.1 L N 
 Hs.22182 ZNF23 Zinc finger protein 23 (KOX 16) 16q22 4.1 L N  
 Hs.183291 ZNF268 Zinc finger protein 268 5 4.0 L N 
 Hs.156000 ZFP161 Zinc finger protein homologous toZfp161 in mouse 18pter-p11.2 4.0 L N 
 Hs.72318  H sapiens moderately similar to zinc finger protein 91 N/A 4.0 L N 
 Hs.64794 ZNF183 Zinc finger protein 183 (RING finger, C3HC4 type) Xq25-q26 4.0 L N 
 *Hs.110956 ZNF20 Zinc finger protein 20(KOX 13) 19p13.3-p13.2 4.0 L PC 
 Hs.184669 ZNF144 Zinc finger protein 144(Mel-18) 17 3.7 L W 
 Hs.23476 CIZ1 Cip1-interacting zinc finger protein 9q34.1 3.4 L PC  
 Hs.31324 ZNF155 Zinc finger protein 155(pHZ-96) 19q13.2-q13.32 3.2 L N 
 Hs.23019 ZNF16 Zinc finger protein 16 (KOX 9) 8q24 3.1 L N  
 Hs.88219 ZNF200 Zinc finger protein 200 16p13.3 3.1 L N 
Activator       
 Hs.146847 TANK TRAF family member-associated NFKB activator 2q24-q31 84.0 H W 
 Hs.40403 CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 Xq13.1 37.8 H W 
 Hs.198468 PPARGC1 Peroxisome proliferative activated receptor, γ, coactivator 1 4p15.1 13.7 I W 
 Hs.82071 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 6q23.3 12.3 I W 
 Hs.3076 MHC2TA MHC class II transactivator 16p13 10.0 I W 
 Hs.283689 ACT Activator of CREM in testis 6q16.1-q16.3 3.9 L W 
 Hs.79093 p100 EBNA-2 coactivator (100 kd) 7q31.3 3.0 L PC 
Enhancer       
 Hs.83958 TLE4 Transducinlike enhancer of split 4, homolog of DrosophilaE(sp1) 9 721.5 VH W  
 Hs.226573 IKBKB Inhibitor of κ light polypeptide gene enhancer in B-cells, kinase β 8p11.2 106.5 VH W 
 Hs.28935 TLE1 Transducinlike enhancer of split 1, homolog of Drosophila E(sp1) 19p13.3 58.4 H W 
 *Hs.75117 ILF2 Interleukin enhancer binding factor 2, 45 kd N/A 52.4 H W 
 Hs.234434 HEY1 Hairy/enhancer-of-split related with YRPW motif 1 8q21 29.9 H PC  
 Hs.81328 NFKBIA Nuclear factor of κ light polypeptide gene enhancer in B cells inhibitor, α 14q13 23.2 I W 
 Hs.332173 TLE2 Transducinlike enhancer of split 2, homolog of Drosophila E(sp1) 19p13.3 18.8 I W 
 Hs.99029 CEBPB CCAAT/enhancer binding protein(C/EBP), β 20q13.1 11.1 I W 
 Hs.256583 ILF3 Interleukin enhancer binding factor 3, 90 kd 19p13 10.0 I PC 
 *Hs.83428 NFKB1 Nuclear factor of κ light polypeptide gene enhancer in B cells 1 (p105) 4q24 9.7 L W 
 Hs.2227 CEBPG CCAAT/enhancer binding protein (C/EBP), γ 19 5.9 L W  
 Hs.9731 NFKBIB Nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor, β 19q13.1 4.6 L W  
 Hs.306 HIVEP1 Human immunodeficiency virus type I enhancer-binding protein 1 6p24-p22.3 3.8 L W 
 Hs.76722 CEBPD CCAAT/enhancer binding protein(C/EBP), δ 8p11.2-p11.1 3.8 L W 
Forkhead       
 Hs.44481 FOXF2 Forkhead box F2 6p25.3 151.3 VH PC 
 Hs.2714 FOXG1B Forkhead box G1B 14q12-q13 67.9 H W  
 Hs.56213  ESTs, highly similar to FXD3_human forkhead box
protein D3 [H sapiens] 		N/A 55.0 H N 
 Hs.239 FOXM1 Forkhead box M1 12p13 25.9 H W 
 Hs.155591 FOXF1 Forkhead box F1 16q24 21.8 I PC 
 Hs.112968 FOXE3 Forkhead box E3 1p32 7.9 L PC 
 Hs.284186 FOXC1 Forkhead box C1 6p25 6.3 L PC 
 *Hs.170133 FOXO1A Forkhead box O1A (rhabdomyosarcoma) 13q14.1 5.7 L PC 
 Hs.96028 FOXD1 Forkhead box D1 5q12-q13 4.5 L PC 
 Hs.120844 LOC55810 FOXJ2 forkhead factor 12pter-p13.31 4.1 L PC 
 Hs.93974 FOXJ1 Forkhead box J1 17q22-17q25 3.3 L PC 
Helix       
 Hs.76884 ID3 Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 1p36.13-p36.12 30.8 H W 
 Hs.198998 CHUK Conserved helix-loop-helix ubiquitous kinase 10q24-q25 10 I W  
 Hs.30956 NHLH1 Nescient helix loop helix 1 1q22 8.2 L W 
 *Hs.34853 ID4 Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 6p22-p21 3.7 L W 
 Hs.46296 NHLH2 Nescient helix loop helix 2 1p12-p11 3.6 L PC  
 Hs.75424 ID1 Inhibitor of DNA binding 1, dominant negative helix-loop-helix protein 20q11 3.3 L W 
Homeobox       
 Hs.55967 SHOX2 Sort stature homeobox 2 3q25-q26.1 220.3 VH PC 
 Hs.125231 HPX42B Hemopoietic progenitor homeobox 10q26 6.3 L PC 
 *Hs.90077 TGIF TG-interacting factor (TALE family homeobox) 18p11.3 4.9 L W 
Leucine       
 Hs.158205 BLZF1 Basic leucine zipper nuclear factor 1(JEM-1) 1q24 3.4 L PC 
Non-POU       
 Hs.172207 NONO Non-POU domain-containing, octamer-binding Xq13.1 19.5 I W 
Nuclear       
 Hs.249247 FBRNP Heterogeneous nuclear protein similar to rat helix destabilizing protein 10 31.4 H PC 
Oncogene       
 Hs.858 RELB v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of κ light polypeptide gene enhancer in B-cells 3) 19q13.2 260.5 VH W  
 Hs.75569 RELA v-rel avian reticuloendotheliosis viral oncogene homolog A (nuclear factor of κ light polypeptide gene enhancer in B-cells 3 [p65]) 11q13 143.6 VH W  
 Hs.198951 JUNB jun B proto-oncogene 19p13.2 56.9 H W 
 Hs.78465 JUN v-jun avian sarcoma virus 17 oncogene homolog 1p32-p31 47.2 H W  
 Hs.300592 MYBL1 v-myb avian myeloblastosis viral oncogene homolog–like 1 8q22 43.0 H W  
 Hs.51305 MAFF v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein F 22q13.1 36.4 H PC  
 Hs.2780 JUND jun D proto-oncogene 19p13.2 20.8 I W 
 *Hs.79070 MYC v-myc avian myelocytomatosis viral oncogene homolog 8q24.12-q24.13 18.3 I W 
 Hs.85146 ETS2 v-ets avian erythroblastosis virus E26 oncogene homolog 2 21q22.2 11.0 I W 
 Hs.179718 MYBL2 v-myb avian myeloblastosis viral oncogene homolog–like 2 20q13.1 9.5 L W 
 Hs.92137 MYCL1 v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived 1p34.3 8.1 L W 
 Hs.724 THRA Thyroid hormone receptor, α (avian erythroblastic leukemia viral [v-erb-a] oncogene homolog) 17q11.2 6.2 L W  
 Hs.2969 SKI v-ski avian sarcoma viral oncogene homolog 1q22-q24 5.3 L W 
 Hs.110713 DEK DEK oncogene (DNA binding) 6p23 4.9 L W 
 *Hs.157441 SPI1 Spleen focus-forming virus (SFFV) proviral integration oncogene spi1 11p11.2 4.5 L W 
 Hs.181128 ELK1 ELK1, member of ETS oncogene family Xp11.2 4.4 L W  
 Hs.431 BMI1 Murine leukemia viral (bmi-1) oncogene homolog 10p13 4.0 L W 
 Hs.1334 MYB v-myb avian myeloblastosis viral oncogene homolog 6q22-q23 3.7 L W  
 Hs.252229 MAFG v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein G 17q25 3.5 L W  
 Hs.30250 MAF v-maf musculoaponeurotic fibrosarcoma (avian) oncogene homolog 16q22-q23 3.1 L W 
PHD       
 Hs.166204 PHF1 PHD finger protein 1 6p21.3 7.2 L PC 
Repressor       
 Hs.144904 NCOR1 Nuclear receptor corepressor 1 17p11.2 21.2 I W 
 Hs.89421 CIR CBF1 interacting corepressor 2p23.3-q24.3 6.7 L W 
 Hs.7222 RBAK RB-associated KRAB repressor 7 6.0 L PC  
 Hs.5710 CREG Cellular repressor of E1A-stimulated genes 1q24 5.1 L PC 
 Hs.287994 NCOR2 Nuclear receptor corepressor 2 12q24 3.7 L W 
Ring       
 *Hs.14084 RNF7 Ring finger protein 7 3q22-q24 401.9 VH PC 
 Hs.216354 RNF5 Ring finger protein 5 6p21.3 396.4 VH N  
 Hs.97176 RNF25 Ring finger protein 25 2p23.3-q34 358.7 VH N 
 Hs.59545 RNF15 Ring finger protein 15 6p21.3 220.9 VH N  
 Hs.8834 RNF3 Ring finger protein 3 4p16.3 58.4 H N 
 Hs.23794 CHFR Checkpoint with forkhead and ring finger domains 12 42.1 H PC  
 Hs.32597 RNF6 Ring finger protein (C3H2C3 type) 6 13q12.2 31.5 H N 
 *Hs.6900 RNF13 Ring finger protein 13 3p13-q26.1 10.4 I N  
 Hs.61515  H sapiens, similar to ring finger protein 23, clone MGC:2475, mRNA, complete cds N/A 6.4 L N  
 Hs.7838 MKRN1 Makorin, ring finger protein, 1 7q34 5.9 L PC 
 Hs.35384 RING1 Ring finger protein 1 6p21.3 4.4 L W  
 Hs.274295 RNF9 Ring finger protein 9 6p21.3 4.3 L PC  
 Hs.59106 CGR19 Cell growth regulatory with ring finger domain 14q21.1-q23.3 4.2 L N  
 Hs.91096 RNF Ring finger protein 6p21.3 4.0 L N 
Others       
 Hs.326876 SOX6 H sapiens SOX6 mRNA, complete cds 11p15.3 98.2 H W 
 Hs.185708 EBF Early B-cell factor 5q34 81.8 H W 
 Hs.288697 MGC11349 Hypothetical protein MGC11349 3p13-q26.1 12.2 I N  
 Hs.23240  H sapiens cDNA: FLJ21848 fis, clone HEP01925 N/A 11.6 I N  
 Hs.278270 P23 Unactive progesterone receptor, 23 kD 12 5.7 L PC 
 Hs.7367  H sapiens BTB domain protein (BDPL) mRNA, partial cds N/A 4.3 L PC 

The genes are presented by general category. UniGene cluster identification number (ID), Gene Name, and Gene Description are abstracted from UniGene (build version 135), Band indicates chromosomal band location; FB, level of expression as measured relative to background (fold over background), as reported previously.17 Abundance category is based on the relative expression level over background, using the following definitions: L, low level (≥ 3-fold to < 10-fold over background); I, intermediate level (≥ 10-fold to < 25-fold); H, high level (≥ 25-fold to < 100-fold); and VH, very high level (≥ 100-fold). Characterization is based on a literature search, as described in the text: W, well-characterized; PC, partially characterized; N, novel; N/A, not available. The asterisk (*) indicates genes that were also selected from the murine stem cell database analysis.

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Selection of genes from the murine stem cell database

The TF category of the murine hematopoietic stem cell database was analyzed to identify the human homologues of known and novel TFs expressed in human bone marrow CD34+ cells, by cross-referencing the murine and human UniGene databases. The murine UniGene clusters corresponding to each of the 161 TFs listed in the murine database were matched with the human clusters in the UniGene database version 129 resulting in 155 homologous human clusters. A total of 145 human genes remained after updating to UniGene version 135 and removing redundant entries. Of these 145 clusters, 87 were represented in the human CD34+ transcriptosome database, including 30 that had already been identified by our search using text descriptors. These 30 clusters are indicated with an asterisk in Table1. Analysis of the remaining 57 human genes for homology to their assigned UniGene cluster or to a corresponding TIGR entry, and excluding those whose known function was obviously not in the category of a transcriptional regulator, resulted in 45 additional genes/ESTs. These additional 45 genes are listed in Table2, and each entry includes the murine gene and its presumed human counterpart, its human UniGene cluster ID and descriptors, its chromosomal location, and the level of expression in human CD34+ cells. Of the 58 clusters that are not present in the CD34+ transcriptosome database, 38 were thought to be unexpressed in human CD34+cells, based on an expression level less than 3-fold over background in the CD34+ transcriptosome database, and the remaining 20 could not be evaluated because they had not been included in the original expression studies that resulted in the CD34+transcriptosome database.

Table 2.

Human TFs identified by homology with murine TFs

Mouse geneMouse gene descriptionHuman UniGene cluster IDHuman geneHuman gene descriptionBandFBAbundanceCharacterization
Nrf-1 Activator involved in nuclear-mitochondrial interactions Hs.180069 NRF1 Nuclear respiratory factor 1 7q32 425.8 VH W 
Dnmt-3b De novo cytosine methyltransferase found in ES cells Hs.251673 DNMT3B DNA (cytosine-5-)methyltransferase 3 β 20q11.2 336.2 VH W  
IFP-35 Associates with B-ATF Hs.50842 IFI35 Interferon-induced protein 35 17q21 191.4 VH PC  
LL2in13291 Homolog of KIAA0326; contains 19 C2H2 zinc fingers Hs.301094 KIAA0326 KIAA0326 protein N/A 126.4 VH N  
Sox-13 SRY related; contains HMG box Hs.201671 SOX13 SRY (sex determining
region Y)-box 13 		1q32 73.3 H PC 
SKIP Interacts with Ski, which may arrest hematopoietic differentiation Hs.79008 SNW1 SKI-INTERACTING PROTEIN 14q21.1-q24.3 40.6 H W 
HPI-BP74/hetero-chromatinic Binds to TIF1 Hs.142442 HP1-BP74 HP1-BP74 1pter-p36.13 39.1 H N 
LL2in10006 Helicase and SNF2 domains; novel helicase Hs.16933 HARP HepA-related protein 2q34-q35 28.6 H W  
Stat-5a Possible role in regulation of endothelial function Hs.181112 HSPC126 HSPC126 protein 13q12.2-q13.3 25.4 H PC  
CtBP2 Potent repressor; interacts with Evi-1, AREB6, ZEB, and FOG Hs.171391 CTBP2 C-terminal binding protein 2 21q21.3 22.2 I W  
HMG-1 Unwinds double-stranded DNA Hs.274472 HMG1 High-mobility group (nonhistone chromosomal) protein 1 13q12 18.1 I W 
HMG-17 Alters interaction between DNA and the histone octamer, maintaining chromatin conformation Hs.181163 HMG17 High-mobility group (nonhistone chromosomal) protein 17 1p36.1 17.9 I W 
LD5-1 Heterochromatosis locus Hs.279586 LOC51578 Adrenal gland protein AD-004 5 17.0 I N  
Heterochromatin protein p25 Regulated during cell cycle Hs.77254 CBX1 Chromobox homolog 1 (Drosophila HP1 β) 17q 16.5 I PC 
Dnmt-3a De novo cytosine methyltransferase found in ES cells Hs.241565 DNMT3A DNA (cytosine-5-)methyltransferase 3 α 2p23 15.0 I W  
SAP1a Ets family; implicated in serum response of fos promoter Hs.169241 ELK4 ELK4, ETS-domain protein (SRF accessory protein 1) 1q32 12.4 I W 
Rpt-1r Down-regulates interleukin 2 receptor Hs.125300 RNF21 Ring finger protein 21, interferon responsive 11p15 11.7 I PC  
Histone H3.3A Nucleosomal histone Hs.181307 H3F3A H3 histone, family 3A 1q41 11.3 I W  
HCNGP Probably involved in regulation of β2-microglobulin genes Hs.27299 HCNGP Transcriptional regulator protein 17 9.8 L N  
HLF bZip; fusion to E2A results in B-lineage leukemia; related to DBP Hs.250692 HLF Hepatic leukemia factor 17q22 8.7 L W  
WBSCR11 Chr 11, Williams-Beuren syndrome region; TFII-I domain Hs.21075 GTF2IRD1 GTF2I repeat domain-containing 1 7q11.23 8.5 L W  
P300/CBP cointegrator Competes against TGIF to promote TGF-β–dependent transcriptional activation Hs.225977 NCOA3 Nuclear receptor coactivator 3 20q12 8.2 L W  
TIP60 Acetylates histones to regulate X-chromosome dosage compensation Hs.6394 HTATIP HIV-1 Tat interactive protein, 60 kd 11 8.2 L W 
CGGBP Can bind the CGG trinucleotide; may affect FMR-1 promoter activity Hs.86041 CGGBP1 CGG triplet repeat binding protein 1 3p12-p11.1 7.2 L PC 
XE169 Similar to jumonji. ARID motif, 2 PHD fingers Hs.283429 SMCX SMC (mouse) homolog, X chromosome Xp11.22-p11.21 6.6 L W  
CPBP? Core promoter element bp? 3 C2H2 zinc fingers Hs.285313 COPEB Core promoter element binding protein 10p15 6.5 L W 
LL2in10261 7 C2H2 zinc fingers Hs.278569 SNX17 Sorting nexin 17 2p23-p22 6.1 L N  
SB1.8/DXS423E Chromosome segregation protein Hs.211602 SMC1L1 SMC1 (structural maintenance of chromosomes 1, yeast)-like 1 Xp11.22-p11.21 6.0 L PC  
HD1 Histone deacetylase; binds to TGIF in a complex that represses TGF-β Hs.88556 HDAC1 Histone deacetylase 1 1p34 5.9 L W  
Erm Ets related Hs.43697 ETV5 Ets variant gene 5 (ets-related molecule) 3q28 5.8 L W  
Ring-box protein-1 Component of VHL tumor suppressor complex and SCF ubiquitin ligase Hs.279919 RBX1 Ring-box 1 22q13.2 5.6 L PC 
SPOP Speckle-type nuclear protein. BTB, Poz domains Hs.129951 SPOP Speckle-type POZ protein 17 5.5 L PC  
NAB-1 Repressor of Krox20; May repress proliferation, differentiation Hs.107474 NAB1 NGFI-A binding protein 1 (ERG1 binding protein 1) 2q32.3-q33 5.4 L W 
Prox1 Homeobox transcription factor required for lymphatic development Hs.110803 LOC51637 CGI-99 protein 14q13.1-q13.3 5.4 L N  
Nmi Interacts with myc, max, and fos Hs.54483 NMI N-myc (and STAT) interactor 2p24.3-q21.3 4.5 L W 
TAK1/TR4 Orphan nuclear receptor; contains C4 zinc finger Hs.520 NR2C2 Nuclear receptor subfamily 2, group C, member 2 3p25 4.2 L W  
LL2in14617 Homologous human uncharacterized protein USF1 contains HLH signature Hs.238954  ESTs, weakly similar to KIAA1204 protein [H sapiens] N/A 4.2 L W 
LL2in10596 KIAA0244; contains TFIIS and PHD motifs Hs.78893 KIAA0244 KIAA0244 protein 6q12 3.8 L N  
Pilot/EGR-3 Zinc finger protein Hs.74088 EGR3 Early growth response 3 8p23-p21 3.8 L W  
CHD-1 Contains chromodomain Hs.22670 CHD1 Chromodomain helicase DNA binding protein 1 5q15-q21 3.7 L W  
HUNKI Contains 2 bromo domains Hs.278675 BRD4 Bromodomain-containing 4 19p13.1 3.7 L PC  
LL1-46 KIAA0518; HLH domain Hs.23763 MGA Max-interacting protein 15q15 3.4 L N  
Nrf-2 A relative of kelch suppresses nrf-2 function Hs.155396 NFE2L2 Nuclear factor (erythroid-derived 2)–like 2 2q31 3.4 L W 
Homeodomain-interact. pk 2 Phosphorylates homeodomain transcription factors Hs.236131 HIPK2 Homeodomain-interacting protein kinase 2 7q32-q34 3.3 L PC  
SWI-SNF(60-kd subunit) Opposes chromatin-dependent repression of transcription Hs.79335 SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 12q13-q14 3.2 L PC 
Mouse geneMouse gene descriptionHuman UniGene cluster IDHuman geneHuman gene descriptionBandFBAbundanceCharacterization
Nrf-1 Activator involved in nuclear-mitochondrial interactions Hs.180069 NRF1 Nuclear respiratory factor 1 7q32 425.8 VH W 
Dnmt-3b De novo cytosine methyltransferase found in ES cells Hs.251673 DNMT3B DNA (cytosine-5-)methyltransferase 3 β 20q11.2 336.2 VH W  
IFP-35 Associates with B-ATF Hs.50842 IFI35 Interferon-induced protein 35 17q21 191.4 VH PC  
LL2in13291 Homolog of KIAA0326; contains 19 C2H2 zinc fingers Hs.301094 KIAA0326 KIAA0326 protein N/A 126.4 VH N  
Sox-13 SRY related; contains HMG box Hs.201671 SOX13 SRY (sex determining
region Y)-box 13 		1q32 73.3 H PC 
SKIP Interacts with Ski, which may arrest hematopoietic differentiation Hs.79008 SNW1 SKI-INTERACTING PROTEIN 14q21.1-q24.3 40.6 H W 
HPI-BP74/hetero-chromatinic Binds to TIF1 Hs.142442 HP1-BP74 HP1-BP74 1pter-p36.13 39.1 H N 
LL2in10006 Helicase and SNF2 domains; novel helicase Hs.16933 HARP HepA-related protein 2q34-q35 28.6 H W  
Stat-5a Possible role in regulation of endothelial function Hs.181112 HSPC126 HSPC126 protein 13q12.2-q13.3 25.4 H PC  
CtBP2 Potent repressor; interacts with Evi-1, AREB6, ZEB, and FOG Hs.171391 CTBP2 C-terminal binding protein 2 21q21.3 22.2 I W  
HMG-1 Unwinds double-stranded DNA Hs.274472 HMG1 High-mobility group (nonhistone chromosomal) protein 1 13q12 18.1 I W 
HMG-17 Alters interaction between DNA and the histone octamer, maintaining chromatin conformation Hs.181163 HMG17 High-mobility group (nonhistone chromosomal) protein 17 1p36.1 17.9 I W 
LD5-1 Heterochromatosis locus Hs.279586 LOC51578 Adrenal gland protein AD-004 5 17.0 I N  
Heterochromatin protein p25 Regulated during cell cycle Hs.77254 CBX1 Chromobox homolog 1 (Drosophila HP1 β) 17q 16.5 I PC 
Dnmt-3a De novo cytosine methyltransferase found in ES cells Hs.241565 DNMT3A DNA (cytosine-5-)methyltransferase 3 α 2p23 15.0 I W  
SAP1a Ets family; implicated in serum response of fos promoter Hs.169241 ELK4 ELK4, ETS-domain protein (SRF accessory protein 1) 1q32 12.4 I W 
Rpt-1r Down-regulates interleukin 2 receptor Hs.125300 RNF21 Ring finger protein 21, interferon responsive 11p15 11.7 I PC  
Histone H3.3A Nucleosomal histone Hs.181307 H3F3A H3 histone, family 3A 1q41 11.3 I W  
HCNGP Probably involved in regulation of β2-microglobulin genes Hs.27299 HCNGP Transcriptional regulator protein 17 9.8 L N  
HLF bZip; fusion to E2A results in B-lineage leukemia; related to DBP Hs.250692 HLF Hepatic leukemia factor 17q22 8.7 L W  
WBSCR11 Chr 11, Williams-Beuren syndrome region; TFII-I domain Hs.21075 GTF2IRD1 GTF2I repeat domain-containing 1 7q11.23 8.5 L W  
P300/CBP cointegrator Competes against TGIF to promote TGF-β–dependent transcriptional activation Hs.225977 NCOA3 Nuclear receptor coactivator 3 20q12 8.2 L W  
TIP60 Acetylates histones to regulate X-chromosome dosage compensation Hs.6394 HTATIP HIV-1 Tat interactive protein, 60 kd 11 8.2 L W 
CGGBP Can bind the CGG trinucleotide; may affect FMR-1 promoter activity Hs.86041 CGGBP1 CGG triplet repeat binding protein 1 3p12-p11.1 7.2 L PC 
XE169 Similar to jumonji. ARID motif, 2 PHD fingers Hs.283429 SMCX SMC (mouse) homolog, X chromosome Xp11.22-p11.21 6.6 L W  
CPBP? Core promoter element bp? 3 C2H2 zinc fingers Hs.285313 COPEB Core promoter element binding protein 10p15 6.5 L W 
LL2in10261 7 C2H2 zinc fingers Hs.278569 SNX17 Sorting nexin 17 2p23-p22 6.1 L N  
SB1.8/DXS423E Chromosome segregation protein Hs.211602 SMC1L1 SMC1 (structural maintenance of chromosomes 1, yeast)-like 1 Xp11.22-p11.21 6.0 L PC  
HD1 Histone deacetylase; binds to TGIF in a complex that represses TGF-β Hs.88556 HDAC1 Histone deacetylase 1 1p34 5.9 L W  
Erm Ets related Hs.43697 ETV5 Ets variant gene 5 (ets-related molecule) 3q28 5.8 L W  
Ring-box protein-1 Component of VHL tumor suppressor complex and SCF ubiquitin ligase Hs.279919 RBX1 Ring-box 1 22q13.2 5.6 L PC 
SPOP Speckle-type nuclear protein. BTB, Poz domains Hs.129951 SPOP Speckle-type POZ protein 17 5.5 L PC  
NAB-1 Repressor of Krox20; May repress proliferation, differentiation Hs.107474 NAB1 NGFI-A binding protein 1 (ERG1 binding protein 1) 2q32.3-q33 5.4 L W 
Prox1 Homeobox transcription factor required for lymphatic development Hs.110803 LOC51637 CGI-99 protein 14q13.1-q13.3 5.4 L N  
Nmi Interacts with myc, max, and fos Hs.54483 NMI N-myc (and STAT) interactor 2p24.3-q21.3 4.5 L W 
TAK1/TR4 Orphan nuclear receptor; contains C4 zinc finger Hs.520 NR2C2 Nuclear receptor subfamily 2, group C, member 2 3p25 4.2 L W  
LL2in14617 Homologous human uncharacterized protein USF1 contains HLH signature Hs.238954  ESTs, weakly similar to KIAA1204 protein [H sapiens] N/A 4.2 L W 
LL2in10596 KIAA0244; contains TFIIS and PHD motifs Hs.78893 KIAA0244 KIAA0244 protein 6q12 3.8 L N  
Pilot/EGR-3 Zinc finger protein Hs.74088 EGR3 Early growth response 3 8p23-p21 3.8 L W  
CHD-1 Contains chromodomain Hs.22670 CHD1 Chromodomain helicase DNA binding protein 1 5q15-q21 3.7 L W  
HUNKI Contains 2 bromo domains Hs.278675 BRD4 Bromodomain-containing 4 19p13.1 3.7 L PC  
LL1-46 KIAA0518; HLH domain Hs.23763 MGA Max-interacting protein 15q15 3.4 L N  
Nrf-2 A relative of kelch suppresses nrf-2 function Hs.155396 NFE2L2 Nuclear factor (erythroid-derived 2)–like 2 2q31 3.4 L W 
Homeodomain-interact. pk 2 Phosphorylates homeodomain transcription factors Hs.236131 HIPK2 Homeodomain-interacting protein kinase 2 7q32-q34 3.3 L PC  
SWI-SNF(60-kd subunit) Opposes chromatin-dependent repression of transcription Hs.79335 SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 12q13-q14 3.2 L PC 

The table presents the murine gene name, the murine UniGene description, the Human UniGene Cluster ID, the name and UniGene description of the human gene, and the chromosome band (Band). FB indicates level of expression as measured relative to background (fold over background), as reported previously.17 Abundance category is based on the relative expression level over background, using the following definitions: L, low level (≥ 3-fold to < 10-fold over background); I, intermediate level (≥ 10-fold to < 25-fold); H, high level (≥ 25-fold to < 100-fold); and VH, very high level (≥ 100-fold). Characterization is based on a literature search, as described in the text: W, well characterized; PC, partially characterized; N, novel; N/A, not available.

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Literature analysis of the TF database

After combining the datasets mined from the human and murine databases, the total number of potential TFs or regulatory proteins was determined to be 330. This includes 106 genes that are recognized as TFs and 224 genes in other categories, which include zinc fingers (90 genes), enhancers (14 genes), activators (8 genes), forkhead (11 genes), oncogenes (20 genes), ring finger (16 genes), and the combination of helix-loop-helix, homeobox, leucine zipper, nuclear, PHD, POU, and repressor categories (21 genes). The remaining 44 cDNAs represent genes that are functionally characterized as transcriptional regulators but lacked any search terms used in our mining protocol. A literature search of each of these 330 genes was performed to determine what was known about each one, emphasizing the discovery of novel genes. The following convention was used to summarize our search results: K = known gene, well characterized; PC = partially characterized, the gene was reported and some preliminary studies have been performed to indicate its function; N = novel gene, no functional information other than its chromosomal location and sequence homology to a known gene or gene family has been reported. These summaries are given in Tables 1 and 2. As a result of the literature search, 165 (50%) of the 330 transcriptional regulators identified were found to be known genes, 86 (26%) have been partially characterized, and 79 (24%) are novel. The partially characterized and novel transcriptional regulators have been further categorized by their relative level of abundance in CD34+ cells, with 92 expressing at low level (≥ 3-fold to < 10-fold over background), 27 expressing at intermediate level (≥ 10-fold to < 25-fold), 28 at high level (≥ 25-fold to < 100-fold), and 18 expressing at very high levels (≥ 100-fold), using the conventions reported in the CD34+ transcriptosome database.17 

In the current study, we emphasized the identification of novel TFs. Based on our literature search of the 106 identified TFs, 78 appear to be well characterized, known genes, whereas 18 have been partially characterized and 7 represent truly novel genes. These 25 partially characterized and novel genes are listed in Table3 along with details of their presumed function and the supporting literature references.

Table 3.

Novel TFs identified by database search

UniGene cluster IDGene nameGene descriptionCharacterizationAvailable function/informationReferences
Hs.2815 POU6F1 POU domain, class 6, transcription factor 1 PC Member of the class IV POU homeodomain family of transcription factors Wey E, Schafer BW. Biochem Biophys Res Commun. 1996.22 
Hs.239720 CNOT2 CCR4-NOT transcription complex, subunit 2 PC May function as a transcription factor Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.108106 ICBP90 Transcription factor PC CCAAT binding protein, may be involved in the regulation of topoisomerase IIα gene expression Hopfner R et al. Gene. 2001.24 
Hs.294101 PBX3 Pre–B-cell leukemia transcription factor 3 PC Member of the homeodomain family of DNA-binding proteins; very strongly similar to murine Pbx3 Knoepfler PS, Kamps MP. Mech Dev. 1997.25 
Hs.249184 TCF19 Transcription factor 19 (SC1) PC Putative transcription factor; may be involved in the later stages of cell cycle progression Teraoka Y et al. Tissue Antigens. 2000.26 
Hs.29417 ZF HCF-binding transcription factor Zhangfei PC Contains a basic domain-leucine zipper (bZIP) region, an acidic activation domain, and a consensus HCF (host cell factor)-binding motif Lu R, Misra V. Nucleic Acids Res. 2000.27 
Hs.155313 DATF1 Death-associated transcription factor 1 PC Protein has 2 zinc finger motifs, nuclear localization signals, and transcriptional activation domains; may be involved in cell death during development Garcia-Domingo D et al. Proc Natl Acad Sci U S A. 1999.28 
Hs.26703 CNOT8 CCR4-NOT transcription complex, subunit 8 PC Similar to S cerevisiae transcriptional regulator Pop2p. The yeast CCR4-NOT protein complex is a global regulator of RNA polymerase II transcription Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.78061 TCF21 Transcription factor 21 PC Involved in epithelial-mesenchymal interactions in kidney and lung morphogenesis, and may play a role in the specification or differentiation of one or more subsets of epicardial cell types Robb L et al. Dev Dyn. 1998.29 
Hs.59506 DMRT2 Doublesex and mab-3 related transcription factor 2 PC May be involved in male sexual development; contains a DNA-binding domain Ottolenghi C et al. Genomics. 2000.30 
Hs.21704 TCF12 Transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) PC Expressed in many tissues, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins Di Rocco G et al. Mol Cell Biol. 1997.31 
Hs.226318 CNOT7 CCR4-NOT transcription complex, subunit 7 PC The protein encoded by this gene binds to an antiproliferative protein, B-cell translocation protein 1, which negatively regulates cell proliferation Prevot D et al. J Biol Chem. 2001.32 
Hs.35841 NFIX Nuclear factor I/X (CCAAT-binding transcription factor) PC The nuclear factor I (NFI) family of transcription/replication proteins is required for the cell type–specific expression of a number of cellular and viral genes. Fletcher CF et al. Mamm Genome. 1999.33 
Hs.100932 TCF17 Transcription factor 17 PC A human homologue of rat zinc finger gene Kid 1; contains a Kruppel-associated box (KRAB) and C2H2 zinc fingers Przyborski SA et al. Cancer Res. 1998.34 
Hs.92282 PITX2 Pairedlike homeodomain transcription factor 2 PC May regulate gene expression and control cell differentiation; member of the homeodomain family of DNA binding proteins Degar BA et al. Exp Hematol. 2001.35 
Hs.97624 HSF2BP Heat shock transcription factor 2 binding protein PC HSF2 binding protein (HSF2BP) associates with HSF2. HSF2BP may therefore be involved in modulating HSF2 activation. Yoshima T et al. Gene. 1998.36 
Hs.20423 CNOT4 CCR4-NOT transcription complex, subunit 4 PC The yeast CCR4-NOT protein complex is a global regulator of RNA polymerase II transcription. Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.2430 TCFL1 Transcription factor–
like 1 		PC May function as a transcription factor Horikawa I et al. Biochem Biophys Res Commun. 1995.37 
Hs.30824 LZTFL1 Leucine zipper transcription factor–
like 1 		N The LZTFL1 gene has 2 transcript isoforms displaying alternative polyadenylation. Kiss H et al. Genomics. 2001.38 
Hs.27299 HCNGP Transcriptional regulator protein N Strongly similar to uncharacterized murineHcngp N/A 
Hs.93748  H sapiens cDNA clone moderately similar to transcription factorBTF3 N N/A N/A 
Hs.173854 PAXIP1L PAX transcription activation domain interacting protein 1 like N N/A N/A 
Hs.268115  ESTs, weakly similar to T08599 probable transcription factor CA150 [H sapiens] N N/A N/A 
Hs.24572  ESTs, weakly similar to TC17_human
transcription
factor 17 [H sapiens] 		N N/A N/A 
Hs.171185 P38IP Transcription factor (p38 interacting protein) N N/A N/A 
UniGene cluster IDGene nameGene descriptionCharacterizationAvailable function/informationReferences
Hs.2815 POU6F1 POU domain, class 6, transcription factor 1 PC Member of the class IV POU homeodomain family of transcription factors Wey E, Schafer BW. Biochem Biophys Res Commun. 1996.22 
Hs.239720 CNOT2 CCR4-NOT transcription complex, subunit 2 PC May function as a transcription factor Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.108106 ICBP90 Transcription factor PC CCAAT binding protein, may be involved in the regulation of topoisomerase IIα gene expression Hopfner R et al. Gene. 2001.24 
Hs.294101 PBX3 Pre–B-cell leukemia transcription factor 3 PC Member of the homeodomain family of DNA-binding proteins; very strongly similar to murine Pbx3 Knoepfler PS, Kamps MP. Mech Dev. 1997.25 
Hs.249184 TCF19 Transcription factor 19 (SC1) PC Putative transcription factor; may be involved in the later stages of cell cycle progression Teraoka Y et al. Tissue Antigens. 2000.26 
Hs.29417 ZF HCF-binding transcription factor Zhangfei PC Contains a basic domain-leucine zipper (bZIP) region, an acidic activation domain, and a consensus HCF (host cell factor)-binding motif Lu R, Misra V. Nucleic Acids Res. 2000.27 
Hs.155313 DATF1 Death-associated transcription factor 1 PC Protein has 2 zinc finger motifs, nuclear localization signals, and transcriptional activation domains; may be involved in cell death during development Garcia-Domingo D et al. Proc Natl Acad Sci U S A. 1999.28 
Hs.26703 CNOT8 CCR4-NOT transcription complex, subunit 8 PC Similar to S cerevisiae transcriptional regulator Pop2p. The yeast CCR4-NOT protein complex is a global regulator of RNA polymerase II transcription Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.78061 TCF21 Transcription factor 21 PC Involved in epithelial-mesenchymal interactions in kidney and lung morphogenesis, and may play a role in the specification or differentiation of one or more subsets of epicardial cell types Robb L et al. Dev Dyn. 1998.29 
Hs.59506 DMRT2 Doublesex and mab-3 related transcription factor 2 PC May be involved in male sexual development; contains a DNA-binding domain Ottolenghi C et al. Genomics. 2000.30 
Hs.21704 TCF12 Transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) PC Expressed in many tissues, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins Di Rocco G et al. Mol Cell Biol. 1997.31 
Hs.226318 CNOT7 CCR4-NOT transcription complex, subunit 7 PC The protein encoded by this gene binds to an antiproliferative protein, B-cell translocation protein 1, which negatively regulates cell proliferation Prevot D et al. J Biol Chem. 2001.32 
Hs.35841 NFIX Nuclear factor I/X (CCAAT-binding transcription factor) PC The nuclear factor I (NFI) family of transcription/replication proteins is required for the cell type–specific expression of a number of cellular and viral genes. Fletcher CF et al. Mamm Genome. 1999.33 
Hs.100932 TCF17 Transcription factor 17 PC A human homologue of rat zinc finger gene Kid 1; contains a Kruppel-associated box (KRAB) and C2H2 zinc fingers Przyborski SA et al. Cancer Res. 1998.34 
Hs.92282 PITX2 Pairedlike homeodomain transcription factor 2 PC May regulate gene expression and control cell differentiation; member of the homeodomain family of DNA binding proteins Degar BA et al. Exp Hematol. 2001.35 
Hs.97624 HSF2BP Heat shock transcription factor 2 binding protein PC HSF2 binding protein (HSF2BP) associates with HSF2. HSF2BP may therefore be involved in modulating HSF2 activation. Yoshima T et al. Gene. 1998.36 
Hs.20423 CNOT4 CCR4-NOT transcription complex, subunit 4 PC The yeast CCR4-NOT protein complex is a global regulator of RNA polymerase II transcription. Albert TK et al. Nucleic Acids Res. 2000.23 
Hs.2430 TCFL1 Transcription factor–
like 1 		PC May function as a transcription factor Horikawa I et al. Biochem Biophys Res Commun. 1995.37 
Hs.30824 LZTFL1 Leucine zipper transcription factor–
like 1 		N The LZTFL1 gene has 2 transcript isoforms displaying alternative polyadenylation. Kiss H et al. Genomics. 2001.38 
Hs.27299 HCNGP Transcriptional regulator protein N Strongly similar to uncharacterized murineHcngp N/A 
Hs.93748  H sapiens cDNA clone moderately similar to transcription factorBTF3 N N/A N/A 
Hs.173854 PAXIP1L PAX transcription activation domain interacting protein 1 like N N/A N/A 
Hs.268115  ESTs, weakly similar to T08599 probable transcription factor CA150 [H sapiens] N N/A N/A 
Hs.24572  ESTs, weakly similar to TC17_human
transcription
factor 17 [H sapiens] 		N N/A N/A 
Hs.171185 P38IP Transcription factor (p38 interacting protein) N N/A N/A 

The table presents 25 novel and poorly characterized genes or ESTs resulting from these studies, which are likely to be TFs. The table presents the UniGene cluster identification (ID) number, the gene name, the UniGene description of the sequence, the literature characterization, additional available functional information about the gene, and the literature citation. Characterization based on literature search is described in the text as: W, well characterized; PC, partially characterized; N, novel; N/A, not available.

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The current report presents our initial attempts to describe the TFs and related regulatory proteins that are present in the human CD34+ transcriptosome. The study is based primarily on the survey of a human CD34+ transcriptosome database, supplemented by homologies identified in a murine stem cell database, referring them to the CD34+ database.

The human CD34+ transcriptosome database was prepared by hybridization of filter arrays, selecting transcripts that are common to both human and baboon bone marrow CD34+antigen–positive cells.17 This database is felt to be an accurate portrayal of the transcriptosome of the CD34+ cell and was estimated to contain 50% to 75% of the transcripts expressed in this tissue. This database contains 15 970 genes/ESTs expressed in CD34+ cells, and lists their relative level of expression; random sampling of selected transcripts verified (by semiquantitative reverse transcriptase–polymerase chain reaction) that most were expressed at the predicted level.

The murine database (http://stemcell.princeton.edu/) was the result of a cDNA library study, subtracting a stem cell–depleted (AA4.1neg) cDNA library from a mouse fetal liver hematopoietic stem cell (ScaposAA4.1posKitposLinneg/lo) cDNA library.18 The subtracted library represents genome-wide gene expression in mouse hematopoietic stem cells devoid of housekeeping genes. Sequence information on each of these clones was compared by BLAST against GenBank nonredundant protein and nucleotide databases, the EST database, Swissprot, and mouse and human DOTS contigs. Each clone was categorized according to its sequence homology to genes of known functions, resulting in a “transcription factor” category containing 161 entries.

The current study reported here was based on the search of UniGene text descriptors in the CD34+ transcriptosome database domains generally present in TFs and their regulatory proteins, whereas the mining of the murine stem cell database relied on homology between the mouse TFs and human genes. The study resulted in the identification of 330 genes that are likely to be transcriptional regulators expressed in human CD34+ cells. Because this transcriptional regulator database was prepared using text descriptors rather than primary sequence analysis, it should only be regarded as a preliminary database survey, limited by the accuracy of the sequence searches compiled by UniGene and by the contents of the databases that were analyzed. Because this study relied heavily on the UniGene database, a considerable number of potential transcriptional regulators might have been missed because of the absence of search terms in the text descriptors, or the simple fact that the UniGene database does not contain complete cDNA sequences for all human genes. This explains in part why the additional 45 TFs from the murine database were not selected during the CD34+ transcriptosome database analysis.

Despite these limitations, we believe that this gene list will prove to be very useful for further studies of normal and malignant hematopoiesis. One of the most striking features of this list is that many of the genes have been assigned functional roles in numerous other tissues besides bone marrow. Also of note is the identification of 165 partially characterized and novel genes, 11 of which are expressed at a very high level in CD34+ cells, suggesting that they have an important role in this tissue but have not been previously recognized as such. Some of the interesting novel or partially characterized genes include zinc finger protein 161 (ZFP161,Hs. 156000), a cell growth regulator protein with a ring finger domain (CGR19, Hs. 59106), zinc finger protein 198 (ZNF 198, Hs.109526), RB-associated CRAB repressor (RBAK,Hs.7222), death-associated transcription factor 1 (DATF1,Hs. 155313), and a p38-interacting protein (P38IP, Hs. 171185). The human ZFP161 protein is highly homologous (98%) to ZF5, a putative murine repressor for MYC, with a growth-inhibitory function.19 We anticipate that bothZFP161 and RBAK20 are associated factors for 2 very functionally important proteins, MYC and RB, respectively, and may play important regulatory roles in cellular functions such as proliferation, differentiation, and apoptosis; to our knowledge, these genes have not been previously evaluated in hematopoiesis or leukemia. Another interesting protein is zinc finger protein 198 (ZNF 198). This gene has not been functionally characterized, but it is reported to be involved in the t(8;13) translocation,21 resulting in a fusion protein with fibroblast growth factor receptor 1 (FGFR1). Studies of these and other novel genes are underway to ascertain their potential role in cell proliferation, differentiation, and apoptosis in the hematopoietic system.

Detailed studies will be required to verify that each of these genes is indeed expressed in hematopoietic CD34+ cells at the predicted level, to obtain the complete coding sequence for the partial cDNAs/ESTs in the database, and to verify the assigned chromosomal location. We predict that some of these genes may be disrupted by chromosomal translocations, thereby contributing to leukemogenesis. Overall, the database here represents a wealth of potential new information to aid in understanding the molecular aspect of normal and malignant hematopoiesis.

Supported by Public Health Service grant P01-75606 (to C.A.W.).

The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked “advertisement” in accordance with 18 U.S.C. section 1734.

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Author notes

Carol A. Westbrook, Department of Medicine, Section of Hematology and Oncology, 900 S Ashland Ave, M/C 734, Chicago, IL 60607; e-mail: cwcw@uic.edu.

Copyright © 2002 The American Society of Hematology
2002
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