Table 4.

Rank-ordered gene lists characterizing each cluster; genes are up-regulated or down-regulated in relation to the other clusters

Cluster and order
P
Gene
Probe set
Description
Up-regulated genes     
    A      
        1   .002  LTBP1  1495_at   Latent transforming growth factor beta binding protein 1  
        2   .003  CASP3  36143_at   Caspase-3, apoptosis-related cysteine protease  
        4   .011  FTO  37242_at   Fatso  
        5   .015  FOXC1  41027_at   Forkhead box C1  
        6   .003  COL4A5  32667_at   Collagen, type IV, alpha 5 (Alport syndrome)  
        11   .015  RASGRP3  34748_at   RAS guanyl-releasing protein 3 (calcium and DAG-regulated)  
        19   .025  MYCN  35158_at   v-myc myelocytomatosis viral-related oncogene, neuroblastoma derived  
    B      
        1   .005  BIA2  36713_at   BIA2  
        2   .003  CXorf6  38916_at   Chromosome X open reading frame 6  
        3   .014  PLOD2  34795_at   Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2  
        4   .011  OPTN  41744_at   Optineurin  
        5   .016  CLIC2  40013_at   Chloride intracellular channel 2  
        6   .017  RHD  37164_at   Rhesus blood group, D antigen  
        7   .021  CDC42BPA  39962_at   CDC42 binding protein kinase alpha (DMPK-like)  
        8   .038  ANK3  36965_at   Ankyrin 3, node of Ranvier (ankyrin G)  
    C      
        1   .003  SDR1  40782_at   Short-chain dehydrogenase/reductase 1  
        2   .01  SDS  40390_at   Serine dehydratase  
        6   .058  SERPINF1  40856_at   Serine (or cysteine) proteinase inhibitor, clade F  
        8   .092  MALT1  38575_at   Mucosa-associated lymphoid tissue lymphoma translocation gene 1  
        9   .051  HERPUD1  39733_at   Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1  
        10   .056  IRF4  37625_at   Interferon regulatory factor 4  
        11   .034  IL10RA  1062_g_at   Interleukin-10 receptor, alpha  
        12   .035  BCS1L  31842_at   BCS1-like (yeast)  
        13   .054  RAB9A  39628_at   RAB9A, member RAS oncogene family  
    D      
        1   .001  RNASEP1  37471_at   Ribonuclease P1  
        2   .006  PGDS  35523_at   Prostaglandin D2 synthase, hematopoietic  
        3   .006  NHP2L1  41746_at   NHP2 nonhistone chromosome protein 2-like 1 (S cerevisiae)  
        4   .010  UNG  37686_s_at   Uracil-DNA glycosylase  
        5   .011  POP1  38513_at   Processing of precursors 1  
        6   .008  HSU79274  31838_at   Protein predicted by clone 23733  
        7   .005  CGI-51  34845_at   CGI-51 protein  
        8   .010  NASP  33255_at   Nuclear autoantigenic sperm protein (histone-binding)  
        9   .010  CDK4  1942_s_at   Cyclin-dependent kinase 4  
    E      
        1   .002  CAPN1  33908_at   Calpain 1, (mu/l) large subunit  
        2   .010  HSF1  40200_at   Heat shock transcription factor 1  
        3   .005  ACTN4  41753_at   Actinin, alpha 4  
        5   .007  TNRC11  40998_at   Trinucleotide repeat containing 11  
        6   .007  G2AN  37040_at   Alpha glucosidase II alpha subunit  
        7   .005  NFIC  440_at   Nuclear factor I/C (CCAAT-binding transcription factor)  
    F      
        1   .001  EPB41L3  41385_at   Erythrocyte membrane protein band 4.1-like 3  
        2   .001  FCGR2A  37688_f_at   Fc fragment of IgG, low affinity IIa, receptor for (CD32)  
        3   .001  HK3  36372_at   Hexokinase 3 (white cell)  
        4   .002  CSPG2  31682_s_at   Chondroitin sulfate proteoglycan 2 (versican)  
        5   .005  PGAM1  41221_at   Phosphoglycerate mutase 1 (brain)  
        6   .003  LILRB1  32475_at   Leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1  
        7   .006  CYBB  37975_at   Cytochrome b-245, beta polypeptide (chronic granulomatous disease)  
        9   .004  CD86  36270_at   CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)  
Down-regulated genes     
    A      
        3   .004  HLA-DPB1  38095_i_at   Major histocompatibility complex, class II, DP beta 1  
        7   .010  HLA-DMA  37344_at   Major histocompatibility complex, class II, DM alpha  
        8   .012  HLA-DPB1  38096_f_at   Major histocompatibility complex, class II, DP beta 1  
    9   .007  CD74  35016_at   CD74 antigen (invariant polypeptide of MHC, class II antigen-associated)  
        12   .001  HLA-DRB3  41723_s_at   Major histocompatibility complex, class II, DR beta 3  
        16   .009  HLA-DRA  37039_at   Major histocompatibility complex, class II, DR alpha  
        20   .007  RAB31  33371_s_at   RAB31, member RAS oncogene family  
    B      
        12   .01  LGALS1  33412_at   Lectin, galactoside-binding, soluble, 1 (galectin 1)  
        34   .046  STX4A  37911_at   Syntaxin 4A (placental)  
        37   .032  PTPRC  40520_g_at   Protein tyrosine phosphatase, receptor type, C  
        40   .036  EMP3  39182_at   Epithelial membrane protein 3  
        44   .026  CORO1A  38976_at   Coronin, actin binding protein, 1A  
        51   .048  INPPL1  36598_s_at   Inositol polyphosphate phosphatase-like 1  
    C      
        3   .015  DNCL1  34891_at   Dynein, cytoplasmic, light polypeptide 1  
        4   .022  RAB9P40  109_at   Rab9 effector p40  
        5   .035  BDH  37211_at   3-hydroxybutyrate dehydrogenase (heart, mitochondrial)  
        7   .018  CGI-87  41590_at   CGI-87 protein  
        12   .035  BCS1L  31842_at   BCS1-like (yeast)  
        14   .027  POP5  39516_at   RNase MRP/RNase P protein-like  
    D      
        24   .047  HOXA10  41448_at   Homeobox A10  
        34   .028   —   32021_at  H sapiens transcribed sequence with weak similarity to protein ref: NP_060265.1(H sapiens) hypothetical protein FLJ20378 
        40   .046  KIAA0669  41788_i_at   KIAA0669 gene product  
        42   .056  HOXA9  37809_at   Homeobox A9  
    E      
        4   .002  DPM1  34879_at   Dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit  
        16   .010  MCP  38441_s_at   Membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)  
        19   .019  STXBP3  37962_r_at   Syntaxin binding protein 3  
        25   .007  PSMC6  949_s_at   Proteasome (prosome, macropain) 26S subunit, ATPase, 6  
        35   .033  CHUK  33770_at   Conserved helix-loop-helix ubiquitous kinase  
        36   .019  COPB  34326_at   Coatomer protein complex, subunit beta  
F      
        50   .019  CCND2  36650_at   Cyclin D2  
        57   .020  ERG  914_g_at   v-ets erythroblastosis virus E26 oncogene like (avian)  
        80   .035  IMPDH2  36624_at   IMP (inosine monophosphate) dehydrogenase 2  
        82   .022  6-SEP  38826_at   Septin 6  
        84
 		 .025
 		RPL17
 		 32440_at
 		 Ribosomal protein L17
 
Cluster and order
P
Gene
Probe set
Description
Up-regulated genes     
    A      
        1   .002  LTBP1  1495_at   Latent transforming growth factor beta binding protein 1  
        2   .003  CASP3  36143_at   Caspase-3, apoptosis-related cysteine protease  
        4   .011  FTO  37242_at   Fatso  
        5   .015  FOXC1  41027_at   Forkhead box C1  
        6   .003  COL4A5  32667_at   Collagen, type IV, alpha 5 (Alport syndrome)  
        11   .015  RASGRP3  34748_at   RAS guanyl-releasing protein 3 (calcium and DAG-regulated)  
        19   .025  MYCN  35158_at   v-myc myelocytomatosis viral-related oncogene, neuroblastoma derived  
    B      
        1   .005  BIA2  36713_at   BIA2  
        2   .003  CXorf6  38916_at   Chromosome X open reading frame 6  
        3   .014  PLOD2  34795_at   Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2  
        4   .011  OPTN  41744_at   Optineurin  
        5   .016  CLIC2  40013_at   Chloride intracellular channel 2  
        6   .017  RHD  37164_at   Rhesus blood group, D antigen  
        7   .021  CDC42BPA  39962_at   CDC42 binding protein kinase alpha (DMPK-like)  
        8   .038  ANK3  36965_at   Ankyrin 3, node of Ranvier (ankyrin G)  
    C      
        1   .003  SDR1  40782_at   Short-chain dehydrogenase/reductase 1  
        2   .01  SDS  40390_at   Serine dehydratase  
        6   .058  SERPINF1  40856_at   Serine (or cysteine) proteinase inhibitor, clade F  
        8   .092  MALT1  38575_at   Mucosa-associated lymphoid tissue lymphoma translocation gene 1  
        9   .051  HERPUD1  39733_at   Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1  
        10   .056  IRF4  37625_at   Interferon regulatory factor 4  
        11   .034  IL10RA  1062_g_at   Interleukin-10 receptor, alpha  
        12   .035  BCS1L  31842_at   BCS1-like (yeast)  
        13   .054  RAB9A  39628_at   RAB9A, member RAS oncogene family  
    D      
        1   .001  RNASEP1  37471_at   Ribonuclease P1  
        2   .006  PGDS  35523_at   Prostaglandin D2 synthase, hematopoietic  
        3   .006  NHP2L1  41746_at   NHP2 nonhistone chromosome protein 2-like 1 (S cerevisiae)  
        4   .010  UNG  37686_s_at   Uracil-DNA glycosylase  
        5   .011  POP1  38513_at   Processing of precursors 1  
        6   .008  HSU79274  31838_at   Protein predicted by clone 23733  
        7   .005  CGI-51  34845_at   CGI-51 protein  
        8   .010  NASP  33255_at   Nuclear autoantigenic sperm protein (histone-binding)  
        9   .010  CDK4  1942_s_at   Cyclin-dependent kinase 4  
    E      
        1   .002  CAPN1  33908_at   Calpain 1, (mu/l) large subunit  
        2   .010  HSF1  40200_at   Heat shock transcription factor 1  
        3   .005  ACTN4  41753_at   Actinin, alpha 4  
        5   .007  TNRC11  40998_at   Trinucleotide repeat containing 11  
        6   .007  G2AN  37040_at   Alpha glucosidase II alpha subunit  
        7   .005  NFIC  440_at   Nuclear factor I/C (CCAAT-binding transcription factor)  
    F      
        1   .001  EPB41L3  41385_at   Erythrocyte membrane protein band 4.1-like 3  
        2   .001  FCGR2A  37688_f_at   Fc fragment of IgG, low affinity IIa, receptor for (CD32)  
        3   .001  HK3  36372_at   Hexokinase 3 (white cell)  
        4   .002  CSPG2  31682_s_at   Chondroitin sulfate proteoglycan 2 (versican)  
        5   .005  PGAM1  41221_at   Phosphoglycerate mutase 1 (brain)  
        6   .003  LILRB1  32475_at   Leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1  
        7   .006  CYBB  37975_at   Cytochrome b-245, beta polypeptide (chronic granulomatous disease)  
        9   .004  CD86  36270_at   CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)  
Down-regulated genes     
    A      
        3   .004  HLA-DPB1  38095_i_at   Major histocompatibility complex, class II, DP beta 1  
        7   .010  HLA-DMA  37344_at   Major histocompatibility complex, class II, DM alpha  
        8   .012  HLA-DPB1  38096_f_at   Major histocompatibility complex, class II, DP beta 1  
    9   .007  CD74  35016_at   CD74 antigen (invariant polypeptide of MHC, class II antigen-associated)  
        12   .001  HLA-DRB3  41723_s_at   Major histocompatibility complex, class II, DR beta 3  
        16   .009  HLA-DRA  37039_at   Major histocompatibility complex, class II, DR alpha  
        20   .007  RAB31  33371_s_at   RAB31, member RAS oncogene family  
    B      
        12   .01  LGALS1  33412_at   Lectin, galactoside-binding, soluble, 1 (galectin 1)  
        34   .046  STX4A  37911_at   Syntaxin 4A (placental)  
        37   .032  PTPRC  40520_g_at   Protein tyrosine phosphatase, receptor type, C  
        40   .036  EMP3  39182_at   Epithelial membrane protein 3  
        44   .026  CORO1A  38976_at   Coronin, actin binding protein, 1A  
        51   .048  INPPL1  36598_s_at   Inositol polyphosphate phosphatase-like 1  
    C      
        3   .015  DNCL1  34891_at   Dynein, cytoplasmic, light polypeptide 1  
        4   .022  RAB9P40  109_at   Rab9 effector p40  
        5   .035  BDH  37211_at   3-hydroxybutyrate dehydrogenase (heart, mitochondrial)  
        7   .018  CGI-87  41590_at   CGI-87 protein  
        12   .035  BCS1L  31842_at   BCS1-like (yeast)  
        14   .027  POP5  39516_at   RNase MRP/RNase P protein-like  
    D      
        24   .047  HOXA10  41448_at   Homeobox A10  
        34   .028   —   32021_at  H sapiens transcribed sequence with weak similarity to protein ref: NP_060265.1(H sapiens) hypothetical protein FLJ20378 
        40   .046  KIAA0669  41788_i_at   KIAA0669 gene product  
        42   .056  HOXA9  37809_at   Homeobox A9  
    E      
        4   .002  DPM1  34879_at   Dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit  
        16   .010  MCP  38441_s_at   Membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)  
        19   .019  STXBP3  37962_r_at   Syntaxin binding protein 3  
        25   .007  PSMC6  949_s_at   Proteasome (prosome, macropain) 26S subunit, ATPase, 6  
        35   .033  CHUK  33770_at   Conserved helix-loop-helix ubiquitous kinase  
        36   .019  COPB  34326_at   Coatomer protein complex, subunit beta  
F      
        50   .019  CCND2  36650_at   Cyclin D2  
        57   .020  ERG  914_g_at   v-ets erythroblastosis virus E26 oncogene like (avian)  
        80   .035  IMPDH2  36624_at   IMP (inosine monophosphate) dehydrogenase 2  
        82   .022  6-SEP  38826_at   Septin 6  
        84
 		 .025
 		RPL17
 		 32440_at
 		 Ribosomal protein L17
 

ANOVA was used to identify rank-ordered gene lists with bootstrap resampling to estimate the stability of these lists. P represents the estimated fraction of time that a gene was ranked at or above its observed position after tabulation of rankings from 1000 bootstrap resamplings (Document S1).44 

— indicates gene symbol not available.

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