Differentially expressed genes in 5q− versus normal CD34+CD38−Thy-1+ cells
| Gene name . | Gene symbol . | Accession no. . | Known function . | Fisher score . |
|---|---|---|---|---|
| Up-regulated | ||||
| Interferon-induced transmembrane protein 1 | IFITM1* | NM_003641 | Inhibition of cell proliferation | 2.7 |
| Serine/threonine kinase 19 | STK19 | NM_032454 | Transcriptional regulation | 2.5 |
| Kelch-like ECT2 interacting protein | KLEIP | NM_014458 | Cytoskeleton organization | 2.0 |
| Kinesin family member 2C | KIF2C | NM_006845 | Chromosome movements during cell division | 2.0 |
| Growth arrest–specific 2 | GAS2 | NM_005256 | p53-dependent apoptosis | 2.0 |
| Cytochrome b-245, beta polypeptide | CYBB | NM_000397 | Microbicidal phagocytic oxidative system | 1.9 |
| Solute carrier family 9 | SLC9A3R1 | NM_004252 | Wnt signaling | 1.9 |
| Gp25L2 protein | HSGP25L2G | BC001123 | Located at 5q35.3; unknown function | 1.9 |
| TAF5 RNA polymerase II | TAF5* | NM_006951 | Transcriptional regulation | 1.8 |
| Thiosulfate sulfurtransferase, rhodanese | TST | NM_003312 | Mitochondrial enzyme | 1.8 |
| Topoisomerase (DNA) II binding protein | TOPBP1 | NM_007027 | DNA damage response protein | 1.7 |
| Golgin-67 | GOLGIN-67 | AF204231 | Golgi apparatus protein | 1.6 |
| CHK2 checkpoint homolog, S pombe | CHEK2 | NM_007194 | Putative tumor suppressor | 1.6 |
| Enah/Vasp-like | EVL | NM_016337 | Cytoskeleton rearrangement and signal transduction | 1.6 |
| Cell division cycle–associated 7 | CDCA7 | NM_031942 | C-myc target gene; lymphoblastoid cell transformation | 1.6 |
| CCAAT/enhancer binding protein (C/EBP), alpha | CEBPA* | NM_004364 | TF; neutrophil differentiation; mutated in AML | 1.5 |
| Cell division cycle 25 B | CDC25B | NM_021874 | Cell cycle regulator; oncogenic properties | 1.5 |
| Polymerase (D directed), epsilon 2, p59 subunit | POLE2 | NM_021874 | Cell cycle regulator; oncogenic properties | 1.5 |
| Polymerase (D directed), epsilon 2, p59 subunit | POLE2 | NM_002692 | DNA replication | 1.5 |
| CD99 antigen | CD99 | NM_002414 | T-cell apoptosis; involved in gastric adenocarcinomas | 1.4 |
| Bloom syndrome | BLM | NM_000057 | Suppressor of inappropriate recombination. | 1.4 |
| Defective in sister chromatid cohesion homolog 1 | DCC1 | NM_024094 | Faithful inheritance of chromosomes to daughter cells | 1.4 |
| D (cytosine-5-)-methyltransferase 3, alpha | DNMT3 | NM_022552 | De novo methylation | 1.4 |
| Inhibitor of DNA binding 1 | ID1 | NM_002165 | Malignant progression | 1.2 |
| Delta-like homolog | DLK1* | NM_003836 | Notch-related differentiation associated | 1.1 |
| Tumor protein p53 binding protein 1 | TP53BP1 | NM_005657 | Tumor suppressor gene | 1.0 |
| V-myc myelocytoma | MYC | NM_002467 | Oncogene | 1.0 |
| B lymphoma Mo-MLV insertion region | BMI1* | NM_005180 | Implicated in HSC self-renewal | 0.9 |
| Down-regulated | ||||
| Solute carrier family 25A, member 4 | SLC25A4 | NM_001151 | Apoptosis inhibitor | 2.4 |
| Ribosomal protein S21 | RPS21 | NM_001024 | Component of the small 40S ribosomal subunit | 2.2 |
| Arachidonate 12-lipooxygenase, 12R type | ALOX12B | NM_001139 | Iron ion binding | 1.9 |
| Amphiregulin schwannoma–derived growth factor | AREG* | NM_001657 | Interacts with EGF/TGF-α; inhibits carcinoma | 1.8 |
| Hepatic leukemia factor | HLF* | M95585 | TF involved in t(17;19) translocation in ALL | 1.7 |
| TAF7 RNA polymerase II | TAF7* | NM_005642 | Located at 5q31; transcriptional regulation | 1.7 |
| Pleckstrin homolog domain | PLEKHA6 | BC010522 | Signal transduction | 1.7 |
| WAS protein family | WASF3 | AB020707 | Member of the Wiskott-Aldrich syndrome protein family | 1.7 |
| Myotrophin | MTPN | AK055660 | Regulation of NFκB | 1.6 |
| Glycoprotein Ib (platelet), beta-polypeptide | GP1BB | L20860 | Associated with Bernard-Soulier or giant platelet disorder | 1.6 |
| Target of myb1-like 1 (chicken) | TOM1L1 | NM_005486 | Signal transduction | 1.6 |
| F-box and leucine-rich repeat protein 5 | FBXL5 | NM_033535 | Proteasome degradation | 1.6 |
| Activated leukocyte cell adhesion molecule | ALCAM* | Y10183 | Associated with tumor progression | 1.6 |
| Zinc finger protein 366 | ZNF366 | NM_152625 | Located at 5q13.2; transcriptional regulation | 1.6 |
| Forkhead box O1A | FOXO1A | NM_002015 | TF; involved in malignant transformation | 1.6 |
| MADS box transcription enhancer factor 2 | MEF2C | L08895 | Located at 5q14; transcriptional regulation | 1.5 |
| CREBB/EP300 inhibitor 1 | CRI1 | NM_014335 | CREBB/EP300 implicated as tumor suppressor gene | 1.5 |
| Endoplasmic reticulum chaperone (SIL1) | SIL1 | NM_022464 | Located at 5q31; enhances nucleotide exchange | 1.5 |
| CDC42 small effector 2 | CDC42SE2* | AK025620 | Located at 5q23.3; Rho GTPase; regulates actin and kinase signaling | 1.5 |
| Tyrosine kinase with Ig/EGF homology domains | TIE | NM_005424 | High expression correlates with shorter survival in CML | 1.4 |
| Transcription factor 8 | TCF8 | NM_030751 | Involved in TGF and BMP signaling | 1.4 |
| Transforming growth factor beta 1 | TGFB1 | NM_000660 | Multifunctional; proliferation/differentiation, transformation | 1.3 |
| Stem cell growth factor | SCGF | NM_002975 | Growth factor for primitive hematopoietic stem cells | 1.3 |
| Suppression of tumorigenicity 13 | ST13 | U17714 | Candidate tumor suppressor gene | 1.3 |
| R binding motif protein 27 | RBM27 | AB037732 | Located at 5q32; unknown function | 1.2 |
| Tumor necrosis factor, alpha-induced protein 8 | TNFAIP8 | NM_014350 | Located at 5q23.1; oncogenic factor in cancer cells | 1.1 |
| Bone morphogenetic protein 6 | BMP6 | NM_001718 | Secreted signaling protein involved in bone formation | 0.9 |
| Gene name . | Gene symbol . | Accession no. . | Known function . | Fisher score . |
|---|---|---|---|---|
| Up-regulated | ||||
| Interferon-induced transmembrane protein 1 | IFITM1* | NM_003641 | Inhibition of cell proliferation | 2.7 |
| Serine/threonine kinase 19 | STK19 | NM_032454 | Transcriptional regulation | 2.5 |
| Kelch-like ECT2 interacting protein | KLEIP | NM_014458 | Cytoskeleton organization | 2.0 |
| Kinesin family member 2C | KIF2C | NM_006845 | Chromosome movements during cell division | 2.0 |
| Growth arrest–specific 2 | GAS2 | NM_005256 | p53-dependent apoptosis | 2.0 |
| Cytochrome b-245, beta polypeptide | CYBB | NM_000397 | Microbicidal phagocytic oxidative system | 1.9 |
| Solute carrier family 9 | SLC9A3R1 | NM_004252 | Wnt signaling | 1.9 |
| Gp25L2 protein | HSGP25L2G | BC001123 | Located at 5q35.3; unknown function | 1.9 |
| TAF5 RNA polymerase II | TAF5* | NM_006951 | Transcriptional regulation | 1.8 |
| Thiosulfate sulfurtransferase, rhodanese | TST | NM_003312 | Mitochondrial enzyme | 1.8 |
| Topoisomerase (DNA) II binding protein | TOPBP1 | NM_007027 | DNA damage response protein | 1.7 |
| Golgin-67 | GOLGIN-67 | AF204231 | Golgi apparatus protein | 1.6 |
| CHK2 checkpoint homolog, S pombe | CHEK2 | NM_007194 | Putative tumor suppressor | 1.6 |
| Enah/Vasp-like | EVL | NM_016337 | Cytoskeleton rearrangement and signal transduction | 1.6 |
| Cell division cycle–associated 7 | CDCA7 | NM_031942 | C-myc target gene; lymphoblastoid cell transformation | 1.6 |
| CCAAT/enhancer binding protein (C/EBP), alpha | CEBPA* | NM_004364 | TF; neutrophil differentiation; mutated in AML | 1.5 |
| Cell division cycle 25 B | CDC25B | NM_021874 | Cell cycle regulator; oncogenic properties | 1.5 |
| Polymerase (D directed), epsilon 2, p59 subunit | POLE2 | NM_021874 | Cell cycle regulator; oncogenic properties | 1.5 |
| Polymerase (D directed), epsilon 2, p59 subunit | POLE2 | NM_002692 | DNA replication | 1.5 |
| CD99 antigen | CD99 | NM_002414 | T-cell apoptosis; involved in gastric adenocarcinomas | 1.4 |
| Bloom syndrome | BLM | NM_000057 | Suppressor of inappropriate recombination. | 1.4 |
| Defective in sister chromatid cohesion homolog 1 | DCC1 | NM_024094 | Faithful inheritance of chromosomes to daughter cells | 1.4 |
| D (cytosine-5-)-methyltransferase 3, alpha | DNMT3 | NM_022552 | De novo methylation | 1.4 |
| Inhibitor of DNA binding 1 | ID1 | NM_002165 | Malignant progression | 1.2 |
| Delta-like homolog | DLK1* | NM_003836 | Notch-related differentiation associated | 1.1 |
| Tumor protein p53 binding protein 1 | TP53BP1 | NM_005657 | Tumor suppressor gene | 1.0 |
| V-myc myelocytoma | MYC | NM_002467 | Oncogene | 1.0 |
| B lymphoma Mo-MLV insertion region | BMI1* | NM_005180 | Implicated in HSC self-renewal | 0.9 |
| Down-regulated | ||||
| Solute carrier family 25A, member 4 | SLC25A4 | NM_001151 | Apoptosis inhibitor | 2.4 |
| Ribosomal protein S21 | RPS21 | NM_001024 | Component of the small 40S ribosomal subunit | 2.2 |
| Arachidonate 12-lipooxygenase, 12R type | ALOX12B | NM_001139 | Iron ion binding | 1.9 |
| Amphiregulin schwannoma–derived growth factor | AREG* | NM_001657 | Interacts with EGF/TGF-α; inhibits carcinoma | 1.8 |
| Hepatic leukemia factor | HLF* | M95585 | TF involved in t(17;19) translocation in ALL | 1.7 |
| TAF7 RNA polymerase II | TAF7* | NM_005642 | Located at 5q31; transcriptional regulation | 1.7 |
| Pleckstrin homolog domain | PLEKHA6 | BC010522 | Signal transduction | 1.7 |
| WAS protein family | WASF3 | AB020707 | Member of the Wiskott-Aldrich syndrome protein family | 1.7 |
| Myotrophin | MTPN | AK055660 | Regulation of NFκB | 1.6 |
| Glycoprotein Ib (platelet), beta-polypeptide | GP1BB | L20860 | Associated with Bernard-Soulier or giant platelet disorder | 1.6 |
| Target of myb1-like 1 (chicken) | TOM1L1 | NM_005486 | Signal transduction | 1.6 |
| F-box and leucine-rich repeat protein 5 | FBXL5 | NM_033535 | Proteasome degradation | 1.6 |
| Activated leukocyte cell adhesion molecule | ALCAM* | Y10183 | Associated with tumor progression | 1.6 |
| Zinc finger protein 366 | ZNF366 | NM_152625 | Located at 5q13.2; transcriptional regulation | 1.6 |
| Forkhead box O1A | FOXO1A | NM_002015 | TF; involved in malignant transformation | 1.6 |
| MADS box transcription enhancer factor 2 | MEF2C | L08895 | Located at 5q14; transcriptional regulation | 1.5 |
| CREBB/EP300 inhibitor 1 | CRI1 | NM_014335 | CREBB/EP300 implicated as tumor suppressor gene | 1.5 |
| Endoplasmic reticulum chaperone (SIL1) | SIL1 | NM_022464 | Located at 5q31; enhances nucleotide exchange | 1.5 |
| CDC42 small effector 2 | CDC42SE2* | AK025620 | Located at 5q23.3; Rho GTPase; regulates actin and kinase signaling | 1.5 |
| Tyrosine kinase with Ig/EGF homology domains | TIE | NM_005424 | High expression correlates with shorter survival in CML | 1.4 |
| Transcription factor 8 | TCF8 | NM_030751 | Involved in TGF and BMP signaling | 1.4 |
| Transforming growth factor beta 1 | TGFB1 | NM_000660 | Multifunctional; proliferation/differentiation, transformation | 1.3 |
| Stem cell growth factor | SCGF | NM_002975 | Growth factor for primitive hematopoietic stem cells | 1.3 |
| Suppression of tumorigenicity 13 | ST13 | U17714 | Candidate tumor suppressor gene | 1.3 |
| R binding motif protein 27 | RBM27 | AB037732 | Located at 5q32; unknown function | 1.2 |
| Tumor necrosis factor, alpha-induced protein 8 | TNFAIP8 | NM_014350 | Located at 5q23.1; oncogenic factor in cancer cells | 1.1 |
| Bone morphogenetic protein 6 | BMP6 | NM_001718 | Secreted signaling protein involved in bone formation | 0.9 |
Selected list of genes up- or down-regulated in 5q− (n=4) CD34+CD38−Thy-1+ candidate HSCs when compared with normal (n=5) CD34+CD38−Thy-1+ cells (for complete list see Table S3).
TF indicates transcription factor; and CML, chronic myelogenous leukemia.
Microarray-based expression validated by Q-PCR.