Table 2

Cluster from supervised shaving applied to full set of 3624 genes

Position

ClonelD

Description


"-685"

"712937"

"hPMSI=DNA mismatch repair protein=mutL homologue"

"-3531"

"1186043"

"Unknown UG Hs.134746 ESTs,"

"1661"

"352820"

"Unknown UG Hs.231825 ESTs"

"-2667"

"1356433"

"Unknown 645"

*"798"

"814622"

"Unknown UG Hs.49614 ESTs"

"-3545"

"713080"

"CLK-2=cdc2/CDC28-like protein kinase-2"

*"-153"

"1339106"

"XE7=B-lymphocyte surface protein"

*"824"

"1356501"

"Unknown UG Hs.130721 ESTs"

"-3414"

"1319801"

"Similar to non-erythropoietic porphobilinogen deaminase (hydroxymethylbilane synt EC4.3.1.8)"

"-1577"

"1353785"

"Unknown UG Hs.119769 ESTs"

"-3242"

"376942"

"Ro ribonucleoprotein autoantigen (Ro/SS-A)=autoantigen calreticulin"

*"-3535"

"1336373"

"Similar to High mobility group (nonhistone chromosomal) protein isoforms I and Y"

"-3412"

"344219"

"5'-terminal region of UMK"

"-673"

"279363"

"Adenosine kinase"

"920"

"1355987"

"Unknown UG Hs.180836 EST"

*"800"

"1358163"

"Phosphatidylinositol 3-kinase p1 10 catalytic, gamma isoform"

*"823"

"1319062"

"WIP/HS PRPL-2=WASP interacting protein"

*"799"

"1339726"

"Unknown 168"

*"788"

"825199"

"Unknown 164"

"-3544"

"1285581"

"Similar to myb-related gene A-myb 5'-region"

"-68"

"589589"

"homolog of Drosophila splicing regulator suppressor-of-white-apricot"

*"759"

"1333557"

"Unknown 161"

"339"

"1336946"

"Unknown 80"

"-178"

"1354703"

"Unknown UG Hs.150458 ESTs"

"-933"

"1184133"

"CASPASE-3=CPP32 isoform alpha=yama=cysteine protease"

"-2714"

"149994"

"B12 protein=tumor necrosis factor-alpha-induced endothelial primary response gene

"-3364"

"271976"

"ACYI =aminoacylase-I"

"-118"

"145409"

"Low-affinity IgG Fc receptor II-B and C isoforms (multiple orthologous genes)"

*"-671"

"1317098"

"tyrosine kinase (TnkI)"

"-2623"

"324973"

"9G8 splicing factor"

*"783"

"814601"

"Unknown UG Hs.161905 EST"

"2421"

"1370055"

"Unknown 602"

"1855"

"1358160"

"Unknown 428"

*"813"

"23173"

"JNK3=Stress-activated protein kinase"

"-1412"

"22438"

"RYK receptor-like tyrosine kinase"

"1104"

"1336779"

"Unknown 221"

"1521"

"1670861"

"Unknown UG Hs.32533 ESTs"

"2568"

"1184568"

"Unknown UG Hs.120785 ESTs"

"-3161"

"365358"

"pM5 protein=homology to conserved regions of the collagenase gene family"

"279"

"1367883"

"KIAA0430"

"338"

"1336591"

"Unknown UG Hs.180644 ESTs"

*"63"

"746300"

"Unknown UG Hs.136345 ESTs"

*"-2661"

"1302032"

"Deoxycytidylate deaminase"

*"787"

"1338448"

"Unknown UG Hs.224323 ESTs, Moderately similar to alternatively spliced product exon 13A [H.sapiens]"

"2567"

"1354788"

"Unknown 627"

*"758"

"1333558"

"Unknown 160"

"-3264"

"704732"

"Unknown 699"

"-2654"

"724397"

"lymphopain=C 1 peptidase expressed in natural killer and cytotoxic T cells"

"1132"

"1354522"

"Unknown UG Hs.125285 ESTs, Highly similar to (defline not available 4200446) [Mlus]"

*"-1595"

"1186040"

"Unknown UG Hs.136589 ESTs"

"-2320"

"241481"

"CASPASE-10=Mch4=FLICE2"

"-3345"

"502761"

"Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase phoribosylaminoimidazole synthetase"

"-33"

"268727"

"MYH=DNA mismatch repair protein=mutY homologue"

*"774"

"701606"

"CDIO=CALLA=Neprilysin=enkepalinase"

"-533"

"276483"

"(2'-5') oligoadenylate synthetase E"

"1388"

"1350824"

"Unknown UG Hs.163773 ESTs"

"-3244"

"488754"

"DAP-1 =putative mediator of the gamma interferon-induced cell death"

"3097"

"686331"

"DCHT=Similar to rat pancreatic serine threonine kinase"

"-2641"

"1355868"

"Unknown 643"

"-3135"

"199018"

"P120=proliferating-cell nudeolar protein"

"-1578"

"713301"

"Unknown UG Hs.32218 ESTs,

"-2502"

"153355"

"LD78 beta=almost identical to MIP-1 alpha=chemokine"

"2328"

"1341026"

"yotiao=protein of neuronal and neuromuscular synapses that interacts with specific variants of NMDA receptor subunit NR 1"

"1863"

"1357676"

"Unknown UG Hs.191211 ESTs"

"1399"

"1356420"

"Unknown UG Hs.207995 ESTs"

"-3401"

"844479"

"Pig8=p53 inducible gene=etoposide-induced mRNA=Similar to El 24 = p53 responsive (sculus)"

"-3040"

"1368740"

"Unknown UG Hs.125307 EST"

"-3193"

"152653"

"C-I-Tetrahydrofolate Synthase, cytoplasmic"

"-3437"

"814765"

"kinase A anchor protein"

"1387"

"1318821"

"Unknown UG Ms. 108614 Homo sapiens mRNAfor KIAA0627 protein, partial cds"

"-2527"

"1357085"

"Acidic 82 kDa protein"

*"1400"

"682995"

"Unknown 298"

*"724"

"1286796"

"Unknown UG Hs.61506 ESTs"

"413"

"1334297"

"Unknown 98"

*"789"

"825217"

"Unknown UG Hs.169565 ESTs,

"-2754"

"1318136"

"5'-AMP-activated protein kinase, gamma-I subunit"

"1052"

"1240803"

"Unknown 211"

"278"

"815671"

"Unknown UG Hs.101340 ESTs"

"-2501"

"346550"

"MIP-1 alpha=LD78 alpha=pAT464=Small inducible cytokine A3=macrophage inflammatory in (GOS 19-1)=chemokine"

"1988"

"1320268"

"Unknown 480"

"-903"

"704637"

"Unknown UG Hs.5354 ESTs"

"-2649"

"181998"

"NFAT3=NFATc4"

"-2648"

"171693"

"Lst-1 =IC7=interferon-gamma-inducible gene present in lymphoid tissues, T cells, macrophages, and histiocyte cell lines

encoding a transmembrane protein"

"2373"

"1338072"

"Unknown 592"

"223"

"1352327"

"Unknown 52"

"1269"

"1339210"

"Unknown 261"

"-3004"

"1289545"

"Unknown UG Hs.187869 ESTs"

"1177"

"700949"

"Similar to myosin-IXb"

*"779"

"703735"

"Unknown UG Hs.28355 ESTs"

*"464"

"685761"

"Unknown III"

"1229"

"700643"

"Unknown UG Hs.104492 ESTs"

"-3482"

"51058"

"E2F-4=pRB-binding transcription factor"

"-3584"

"1358191"

"Similar to DNA polymerase beta=DNA alkylation repair protein"

*"-429"

"35356"

"Neurotrophic tyrosine kinase, receptor, type 3 (TrkC)"

"-3136"

"265590"

"NFI =Neurofibromin"

"956"

"1289384"

"Unknown 198"

"2491"

"814251"

"SLAM=signaling lymphocytic activation molecule"

"2083"

"1353083"

"Unknown UG Hs.136972 EST"

"1102"

"1372068"

"KIAA0603=Similar to TBCI"

"-1010"

"595474"

"Pak 1 =p21-activated protein kinase"

"-3594"

"1269836"

"BCL-7B"

"-2270"

"265267"

"HSP70"

"-944"

"1337124"

"Unknown UG Hs.81248 CUG triplet repeat, RNA-binding protein 1"

"-3330"

"1301224"

"Elongin B=RNA polymerase II transcription factor SIII pi 8 subunit"

"1658"

"1241118"

"Unknown 346"

"-3140"

"841361"

"GR02=GRO beta=MIP2 alpha=macrophage inflammatory protein-2 alpha=chemokine"

"-2651"

"525540"

"BCL-3"

"-3350"

"1186114"

"Unknown UG Hs.116447 EST"

"-2990"

"1289569"

"Unknown UG Hs.146165 ESTs"

*"809"

"1270618"

"Unknown UG Hs.208970 EST, Weakly similar to neuronal thread protein AD7c-NTP [ens]"

"-3160"

"703707"

"Protein disulfide isomerase-related protein (PDIR)"

"874"

"1320313"

"Unknown UG Hs.132458 ESTs"

"-3390"

"1339763"

"Unknown 710"

"1343"

"1318717"

"LOK=lymphocyte oriented kinase=STE20-like protein kinase that is expressed predominantly in lymphocytes"

"-179"

"301551"

"Integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"

*"723"

"824754"

"Unknown UG Hs.145058 ESTs"

"-3406"

"1300230"

"Unknown UG Hs.56421 ESTs, Weakly similar to Similarity to H.influenza ribonucl H [C.elegans]"

"-573"

"1341161"

"Similar to rhoGap protein"

*"722"

"1341225"

"Unknown UG Hs.186709 ESTs,! [H.sapiens]"

"2212"

"1350784"

"Unknown UG Hs.163202 EST"

"-3478"

"417897"

"cleavage stimulation factor 77kDa subunit=polyadenylation factor subunit=homolog the Drosophila suppressor of forked protein"

"-887"

"756965"

"RGS14=regulator of G protein signaling"

"1344"

"825333"

"Unknown UG Hs.193017 ESTs, Highly similar to (defline not available 4220898) [ens]"

*"743"

"1358192"

"Unknown UG Hs.228205 EST,

"1850"

"1353072"

"Unknown 426"

"-3391"

"1340604"

"Unknown UG Hs.127121 ESTs"

"-236"

"686771"

"tubulin-gamma"

"-3343"

"293934"

"CAS=chromosome segregation gene homolog"

"2566"

"1350728"

"Unknown 626"

"-2984"

"955354"

"putative cell surface ligand for T1/ST2 receptor (related to IL-1 receptors)"

"-3149"

"366713"

"GSK3=glycogen synthase kinase 3"

*"720"

"815539"

"JAWI=lymphoid-restricted membrane protein"

"-3177"

"378364"

"PRODH=proline dehydrogenase/proline oxidase=p53-induced gene"

"1268"

"1339305"

"Unknown 260"

"-3616"

"1302092"

"Unknown UG Hs.214428 ESTs"

"1210"

"685368"

"Unknown 243"

"2330"

"1240688"

"Unknown 577"

"259"

"1369262"

"KIAAOO 19=similar to transforming protein tre"-2528" "1184411" "MINOR=mitogen induced nuclear orphan receptor=NOR-l=Nur77 orphan nuclear receptor family member"

"-3586"

"1309295"

"Unknown UG Hs.136985 ESTs"

"2045"

"1352570"

"Unknown 494"

"2067"

"1320316"

"Unknown 508"

"-3533"

"298303"

"TECK chemokine"

"-3530"

"1355240"

"Unknown UG Hs.130849 ESTs"

*"-2469"

"417226"

"c-myc"

"1784"

"1355354"

"Unknown 394"

"-3023"

"700772"

"Smad2=Madr2=JV 18-1 =Homologue of Mothers Against Decapentaplegic (MAD)=Activated beta"

*"793"

"1353041"

"Unknown 166"

"-3162"

"1289546"

"Similar to arginine/aspartate-rich 37.3 K protein"

*"-2669"

"1186215"

"Unknown UG Hs.190288 EST"

"-113"

"1337185"

"KIAA0037"

"-3434"

"1338032"

"CPR2=cell cycle progression 2"

"-2621"

"1338456"

"c-myc binding protein"

"1333"

"824376"

"Similar to (AFO 16450) Similar to acyltransferase"

"-3405"

"1334813"

"Unknown UG Hs.17883 protein phosphatase IG (formerly 2C), magnesium-dependent, isoform"

"2301"

"300051"

"myosin light chain-2"

"1144"

"1372011"

"Unknown UG Hs.209146 ESTs"

"-3436"

"485171"

"methionine adenosyltransferase alpha subunit"

"1339"

"1355713"

"Unknown 277"

"1156"

"1351290"

"Similar to (Z49125) C47G2.4"

*"721"

"1353015"

"Unknown 154"

"-3125"

"86040"

"Cytochrome P450, subfamily 1, polypeptide 2 (aromatic compound-inducible)"

"258"

"1367988"

"Unknown 61"

"-3258"

"1304523"

"APRT=adenine phosphoribosyltransferase"

"-3548"

"1340120"

"Unknown 733"

"151 1"

"1351701"

"Unknown UG Hs.124230 ESTs"

"-3280"

"826594"

"replication factor C"

"-3363"

"293035"

"APEX=apurinic endonuclease=DNA alkylation repair protein"

"1190"

"1371313"

"Similar to G-protein coupled receptor pH218"

"1321"

"1309301"

"Unknown UG Hs.136987 EST"

"-3180"

"591683"

"GADD45 alpha=growth arrest and DNA-damage-inducible protein alpha"

"1748"

"1371159"

"Unknown 377"

"-2781"

"1288183"

"BAK=BCL-2 family member"

"108"

"1370125"

"Unknown 22"

"-2941"

"742132"

"Interferon-induced 17 KD protein"

"-2994"

"1271685"

"Unknown UG Hs.176669 ESTs"

"1287"

"1353226"

"Unknown UG Hs.30209 Homo sapiens mRNA for KIAA0854 protein, complete cds"

"1039"

"1671442"

"Unknown UG Hs.171096 ESTs, Weakly similar to (defline not available 4456988) [ens]"

*"83"

"52408"

"ABR=guanine nucleotide regulatory protein"

"3624"

"1355859"

"Similar to myosin IE heavy chain"

"-2746"

"1350736"

"IRF-3=interferon regulatory factor-3"

"1303"

"665682"

"Jnkk2=JNK kinase 2=MAP kinase kinase"

"877"

"1367968"

"Unknown UG Hs.105072 ESTs"

"-3344"

"1341245"

"CD73=5' nudeotidase"

"1191"

"1371317"

"Similar to arylacetyltransferase"

*"-310"

"154493"

"HNPP=nuclear phosphoprotein"

"1976"

"1334933"

"Unknown UG Hs.144684 ESTs"

"-2609"

"1670958"

"SRF=c-fos serum response element-binding transcription factor"

"405"

"701689"

"putative tumor suppressor (LUCA15)"

"-3319"

"1307997"

"Similar to bromodeoxyuridine-sensitive transcript protein=px 19"

"-3255"

"810743"

"MLF2=myelodysplasia/myeloid leukemia factor 2"

"2150"

"1353466"

"Unknown UG Hs.124360 EST"

"-2650"

"511407"

"69 kDa 2'5' oligoadenylate synthetase (P69 2-5A synthetase)"

"252"

"1356345"

"Unknown UG Hs.49500 Homo sapiens mRNA for KIAA0746 protein, partial cds"

"1337"

"1367875"

"Unknown UG Hs.128127 ESTs"

"1302"

"1351266"

"Unknown UG Hs.134197 ESTs, Moderately similar to FAM [M.musculus]"

"1386"

"815165"

"Unknown UG Hs.188732 ESTs"

"-3147"

"549277"

"cell cycle protein p38-2G4 homolog (hG4-l)"

"-3349"

"1355524"

"Similar to rapamycin-binding protein (FKBP25)"

"-173"

"1287032"

"Similar to Drosophila female sterile homeotic (FSH) homologue"

*"777"

"1352112"

"FMR2=Fragile X mental retardation 2=putative transcription factor=LAF-4 and AF-4 ogue"

"-3334"

"346948"

"nm23-H2=NDP kinase B=Nucleoside dephophate kinase B"

"-3256"

"1303575"

"Unknown UG Hs.123304 ESTs"

"1289"

"704690"

"Dyrk6=Ser/Thr protein kinase"

"1133"

"1351498"

"Unknown UG Hs.189063 ESTs"

"2058"

"1339890"

"Unknown 503"

"-2927"

"342647"

"MAPKAP kinase (3pK)"

"1324"

"687198"

"Unknown UG Hs.125860 ESTs"

"-3047"

"203704"

"flavin-containing monooxygenase (FMO 1)"

"-2662"

"1288102"

"Similar to nuclear-encoded mitochondrial NADH-ubiquinone reductase 24Kd subunit"

"1852"

"1371200"

"Similar to (Z78012) C52E4.6"

"1383"

"1319529"

"Unknown 293"

"-3360"

"1671396"

"Similar to friend of GATA-1 (FOG)=zinc finger GATA-I coactivator in erythroid and megakaryocyte lineages"

"1228"

"1336501"

"Unknown 249"

"1353"

"1356762"

"Unknown UG Hs.127480 ESTs"

*"-575"

"490387"

"zinc finger protein 42 MZF-1"

"1242"

"1031754"

"Protein-tyrosine phosphatase 2C"

"1211"

"1372274"

"Unknown UG Hs.208983 ESTs,

"-2759"

"489438"

"MyD88=myeloid differentiation primary response protein=death domain-containing p

"1227"

"1334962"

"Similar to KIAA0437"

"260"

"1341211"

"Unknown UG Hs.191209 ESTs"

"-3137"

"1250770"

"Purine nucleoside phophorylase=lnosine phosphorylase=PNP"

"1385"

"1371029"

"Unknown 295"

"1808"

"1372833"

"Unknown 403"

"-2762"

"1184153"

"Unknown UG Hs.230206 EST"

"1046"

"1352940"

"Unknown 208"

"-2766"

"756452"

"tyk2=non-receptor protein tyrosine kinase"

"1204"

"1370570"

"Lamin B receptor (LBR)"

"1201"

"1241671"

"Similar to (AE000860) conserved protein [Methanobacterium thermoautotrophicum]"

*"735"

"686893"

"Unknown UG Hs.226955 ESTs"

"1338"

"1370103"

"Unknown 276"

"255"

"1338624"

"Unknown UG Hs.192864 ESTs"

"1200"

"1352335"

"Unknown UG Hs.99701 ESTs"

"2133"

"1340880"

"Cancer associated surface antigen (RCASI)"


Genes are ordered from strongest to weakest correlation with survival. The first number is the position in the hierarchical clustering ordering (a minus sign indicates the sign of the gene is to be flipped before averaging); * indicates a gene that also falls in the 380 gene cluster from Alizadeh et al. [14].

Hastie et al. Genome Biology 2000 1:research0003.1-research0003.21   doi:10.1186/gb-2000-1-2-research0003

Open Data