Web Table 4
Hierarchical Clustering           SVD (eigengene 2) SAM (GIST)
GIST cluster panel c, figure 3
(Listed as appears in gene cluster - see web figure 6 for hierarchical relationship) Projection Rank order projection Correlation Rank order correlation Score(d) Numerator(r) Denominator(s+s0) Rank order
 SPRY1 sprouty (Drosophila) homolog 1 (antagonist of FGF signaling) Hs.88044 -5.2211 168 -0.4737 468 3.029284467 2.877141944 0.949776086 40
 EXTL3 exostoses (multiple)-like 3 Hs.9018 -1.773 1308 -0.3206 1039 1.552046871 1.210679444 0.780053404 386
 Homo sapiens cDNA FLJ20848 fis, clone ADKA01732 Hs.325825 -1.4999 1492 -0.2046 1596 1.775291285 1.533454444 0.863776247 281
 Homo sapiens cDNA FLJ20848 fis, clone ADKA01732 Hs.325825 -1.7416 1342 -0.1982 1632 2.128176789 1.935148247 0.909298634 170
 HSPA8 heat shock 70kD protein 8 Hs.180414 -1.1611 1753 -0.2152 1540 1.414560606 1.1074225 0.782873845 478
 SLC4A4 solute carrier family 4, sodium bicarbonate cotransporter, member 4 Hs.5462 -8.1948 33 -0.6492 126 2.865987045 2.96130363 1.033257856 54
 TTC1 tetratricopeptide repeat domain 1 Hs.7733 -6.7213 65 -0.7007 78 3.007275211 2.622198333 0.871951567 41
 ESTs Hs.25144 -4.8169 216 -0.637 138 2.31533427 1.921638333 0.829961513 120
 **ESTs Hs.46564 -4.7827 222 -0.5723 241 2.552613927 2.151425889 0.842832465 87
 ESTs Hs.18672 -3.5826 492 -0.6045 185 2.188077954 1.630432901 0.745143882 151
 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 Hs.205353 -4.2327 325 -0.6274 153 2.044795712 1.650828302 0.807331653 193
 Homo sapiens cDNA FLJ12141 fis, clone MAMMA1000348 Hs.7514 -4.9363 197 -0.7157 61 1.94438841 1.59360966 0.819594301 222
 ESTs Hs.145053 -5.053 183 -0.7208 58 2.292927024 1.834613765 0.800118689 125
 PMM1 phosphomannomutase 1 Hs.75835 -3.7885 429 -0.7138 65 1.769273572 1.323863889 0.748252791 287
 DNAJB12 DnaJ (Hsp40) homolog, subfamily B, member 12 Hs.7960 -3.7324 448 -0.6369 139 1.804618812 1.403626111 0.777796453 269
 ESTs Hs.290825 -9.5864 18 -0.76 29 2.850981977 2.891363673 1.014164136 55
 CEP2 Cdc42 effector protein 2 Hs.12289 -6.0351 101 -0.6261 155 2.828404099 2.525825 0.893021263 57
 CEP2 Cdc42 effector protein 2 Hs.12289 -6.3512 84 -0.6813 94 2.76141275 2.421284185 0.87682806 63
 Homo sapiens mRNA; cDNA DKFZp762M127 (from clone DKFZp762M127) Hs.22483 -4.6282 241 -0.6599 115 2.244557041 1.807473333 0.805269503 135
 Homo sapiens WWp2-like mRNA complete cds Hs.333382 -5.6274 137 -0.5578 265 2.872560392 2.629482778 0.915379459 52
 ESTs Hs.9094 -9.5228 19 -0.6844 89 3.753180497 3.782223789 1.007738315 20
 GUCY1A3 guanylate cyclase 1, soluble, alpha 3 Hs.75295 -8.826 26 -0.5948 201 3.324363242 3.67341 1.104996576 31
 GUCY1A3 **guanylate cyclase 1, soluble, alpha 3 Hs.75295 -9.7795 15 -0.6513 125 3.618511962 3.954415556 1.092829206 25
 ESTs Hs.22247 -11.033 7 -0.7266 53 3.845043367 4.093676235 1.064663215 15
 FLJ20898 hypothetical protein FLJ20898 Hs.25549 -5.737 122 -0.5803 230 2.870689819 2.572611667 0.896164974 53
 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta Hs.77439 -4.9423 196 -0.4648 486 3.157508378 2.884961111 0.913682805 38
 CUL5 cullin 5 Hs.101299 -2.717 796 -0.4253 624 2.198284362 1.695891728 0.771461489 146
 CUL5 cullin 5 Hs.101299 -2.0939 1118 -0.3593 886 1.912870517 1.464312833 0.765505464 226
 KIAA0952 KIAA0952 protein Hs.7935 -2.7952 770 -0.2963 1145 2.489776708 2.284232778 0.917444834 96
 MYO6 **myosin VI Hs.22564 -2.7011 808 -0.3732 826 2.103424647 1.747878889 0.830968151 178
 MYO6 myosin VI Hs.22564 -3.9238 392 -0.3945 736 2.651718428 2.461366944 0.928215801 79
 FLJ11149 hypothetical protein FLJ11149 Hs.37558 -3.0101 680 -0.5589 260 1.945649714 1.422544611 0.731141171 221
 KDELR2 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 Hs.118778 -5.3316 155 -0.6597 116 2.686741855 2.209509506 0.822375064 75
 LMO2 LIM domain only 2 (rhombotin-like 1) Hs.184585 -6.6644 68 -0.6251 157 2.697591922 2.574071667 0.954210919 73
 ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 Hs.139336 -5.9614 107 -0.5953 200 2.78496503 2.560810031 0.919512455 60
 GG2-1 TNF-induced protein Hs.17839 -7.2016 48 -0.7668 25 2.961692373 2.572487778 0.868587096 44
 STK17A serine/threonine kinase 17a (apoptosis-inducing) Hs.9075 -6.638 70 -0.7242 56 2.56133594 2.294821667 0.895947162 85
 MGC11257 hypothetical protein MGC11257 Hs.334368 -3.6894 460 -0.5867 216 1.715073341 1.384350764 0.807167094 307
 THG-1 TSC-22-like Hs.102447 -4.5637 255 -0.6669 107 2.495415728 1.8938695 0.758939474 95
 THG-1 TSC-22-like Hs.102447 -4.9941 189 -0.7174 59 2.240670094 1.774562431 0.791978451 138
 CSTF1 cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD Hs.172865 -4.5478 258 -0.4863 438 3.347593384 2.766113889 0.826299246 29
 NUDT4 nudix (nucleoside diphosphate linked moiety X)-type motif 4 Hs.92381 -3.8906 402 -0.56 257 2.485841233 1.92924321 0.77609269 97
 FLJ14054 hypothetical protein FLJ14054 Hs.13528 -9.0254 23 -0.5811 227 3.973809757 4.278678889 1.076719609 11
 MGAT4A mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A Hs.177576 -6.2205 90 -0.8039 11 2.712487721 2.160495531 0.796499654 70
 MGAT4A mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A Hs.177576 -6.0388 99 -0.8074 9 2.333791634 1.904214643 0.815931729 115
 CTSL cathepsin L Hs.78056 -9.6895 16 -0.8198 7 3.322875005 3.188869722 0.959671886 32
 NEK6 NIMA (never in mitosis gene a)-related kinase 6 Hs.9625 -4.6373 240 -0.6081 181 2.125824663 1.807762253 0.850381635 171
 MAGEA10 melanoma antigen, family A, 10 Hs.18048 -3.7553 441 -0.6615 112 1.984198516 1.490168889 0.751018044 211
 PCAF p300/CBP-associated factor Hs.199061 -6.8348 61 -0.7683 24 2.580154283 2.256867389 0.874702495 84
 KIAA0353 KIAA0353 protein Hs.10587 -11.6078 4 -0.7134 66 3.97846006 4.387667269 1.102855678 10
 FLJ20004 **hypothetical protein FLJ20004 Hs.17311 -5.6154 138 -0.6235 159 2.601361273 2.278207778 0.875775234 83
 FKBP8 **FK506-binding protein 8 (38kD) Hs.173464 -4.6108 244 -0.7715 21 1.963870543 1.512340321 0.770081473 215
 FLJ20208 hypothetical protein FLJ20208 Hs.131776 -4.6186 243 -0.7557 33 2.132439058 1.634012708 0.766264669 168
 RBPMS RNA-binding protein gene with multiple splicing Hs.80248 -9.6309 17 -0.7748 19 3.076444383 3.133027778 1.018392465 39
 ESTs Hs.44841 -3.7791 434 -0.6613 113 2.270833438 1.647356667 0.725441434 129
 Homo sapiens cDNA FLJ11177 fis, clone PLACE1007402 Hs.26243 -13.9112 1 -0.8048 10 3.899763294 4.530972531 1.161858346 14
 FLJ20898 hypothetical protein FLJ20898 Hs.25549 -8.3926 31 -0.7145 64 3.711166339 3.373423457 0.908992793 22
 Homo sapiens cDNA: FLJ22050 fis, clone HEP09454 Hs.173705 -1.9959 1174 -0.3973 729 1.718076157 1.261173889 0.734061691 306
 CLN5 ceroid-lipofuscinosis, neuronal 5 Hs.30213 -3.2631 586 -0.6131 174 2.066080038 1.490753889 0.721537337 190
 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide Hs.78989 -3.3398 558 -0.5599 258 2.172873736 1.630677778 0.750470564 155
 AMPD3 adenosine monophosphate deaminase (isoform E) Hs.83918 -11.0426 6 -0.7624 28 3.843662211 3.973048333 1.033662199 16
 AMPD3 adenosine monophosphate deaminase (isoform E) Hs.83918 -4.7956 218 -0.6923 84 2.26139622 1.808568426 0.799757429 132
 ESTs, Moderately similar to I38022 hypothetical protein [H.sapiens] Hs.238797 -5.9317 111 -0.7244 55 2.751335009 2.254387222 0.819379397 65
 ESTs, Moderately similar to I38022 hypothetical protein [H.sapiens] Hs.238797 -5.0218 185 -0.7171 60 2.376866848 1.882160988 0.791866397 106
 NIFU nitrogen fixation cluster-like Hs.9908 -4.1396 350 -0.7301 50 2.532697781 1.759934444 0.694885295 91
 CA2 carbonic anhydrase II Hs.155097 -12.5945 3 -0.74 41 4.971191811 5.109867932 1.027895951 4
 PRKCQ protein kinase C, theta Hs.211593 -13.0635 2 -0.7849 14 5.821060741 5.318023002 0.913583149 1
 ESTs Hs.3991 -6.2373 87 -0.7562 32 3.295569681 2.499965679 0.758583772 33
 FLJ14466 hypothetical protein FLJ14466 Hs.55148 -4.8481 210 -0.6544 121 2.42573207 1.955061265 0.805967522 101
 TMEM2 transmembrane protein 2 Hs.160417 -6.1803 94 -0.7518 34 2.511522387 2.131032778 0.848502402 94
 CHN2 chimerin (chimaerin) 2 Hs.286055 -5.6437 134 -0.6276 151 2.947312169 2.4959075 0.846841921 46
 CD81 CD81 antigen (target of antiproliferative antibody 1) Hs.54457 -4.5803 251 -0.7017 76 2.346457485 1.793145556 0.764192647 112
108962 -5.1136 178 -0.7101 69 2.707084995 2.074546667 0.766339687 71
 SE57-1 CTCL tumor antigen se57-1 Hs.30315 -8.864 25 -0.6949 83 3.904462483 3.634148403 0.930767915 13
 FLJ10261 hypothetical protein FLJ10261 Hs.26176 -7.9389 39 -0.4429 553 4.260083643 4.902848333 1.150880768 6
 PDE1A **phosphodiesterase 1A, calmodulin-dependent Hs.41717 -3.6077 487 -0.5533 279 2.364269984 1.802711597 0.762481277 108
 PROML1 prominin (mouse)-like 1 Hs.112360 -5.7604 120 -0.5606 254 3.936381515 3.204291667 0.81401959 12
 Homo sapiens clone 24421 mRNA sequence Hs.10684 -6.6333 71 -0.4284 608 4.303026608 4.436712153 1.031067794 5
  **ESTs, Moderately similar to I54375 gene NF2 protein [H.sapiens] Hs.136398 -5.7273 126 -0.4547 514 3.615559652 3.450077401 0.95423053 26
 KIAA1492 KIAA1492 protein Hs.91625 -9.9574 13 -0.6355 140 5.448332683 4.96473321 0.911238997 3
 ESTs Hs.49776 -11.3734 5 -0.632 146 5.680857192 5.609222963 0.987390243 2
 ESTs, Hs.13702 -6.394 83 -0.7146 63 3.44925225 2.730875333 0.791729667 27
  **ESTs,  Hs.13702 -6.9915 53 -0.7064 71 3.835456227 3.08069858 0.80321568 17
 SLC12A2 **solute carrier family 12, member 2 Hs.110736 -5.958 108 -0.5842 218 3.814663732 3.138963889 0.822867783 19
 KIAA0229 KIAA0229 protein Hs.20060 -5.955 109 -0.6232 161 3.750965872 2.981031111 0.794736933 21
 KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Hs.81665 -7.7164 41 -0.5996 194 4.127845389 3.714201778 0.899791884 9
 Homo sapiens mRNA; cDNA DKFZp547G133 (from clone DKFZp547G133) Hs.303172 -4.7894 219 -0.5038 395 3.224594571 2.731975 0.84723054 34
 SPRY4 sprouty (Drosophila) homolog 4 Hs.285814 -5.9491 110 -0.4918 427 4.171412012 3.687083333 0.883893349 8
 INPP5A inositol polyphosphate-5-phosphatase, 40kD Hs.124029 -3.3987 541 -0.5212 348 2.512154537 1.884601667 0.750193365 92
 PTP4A3 protein tyrosine phosphatase type IVA, member 3 Hs.43666 -7.3935 46 -0.5576 267 4.211583793 3.946225 0.936993111 7
 PTP4A3 **protein tyrosine phosphatase type IVA, member 3 Hs.43666 -6.8079 62 -0.5811 228 3.828236735 3.440138333 0.898622152 18
 FUS1 lung cancer candidate Hs.8186 -2.8345 753 -0.5501 287 1.956978448 1.413289444 0.722179361 218
 ESTs, Weakly similar to T46371 hypothetical protein DKFZp434P1018.1 [H.sapiens] Hs.23438 -3.9424 388 -0.5301 328 2.71854462 2.129367778 0.783274905 67
 **ESTs, Moderately similar to T46371 hypothetical protein DKFZp434P1018.1 [H.sapiens] Hs.118913 -4.1945 335 -0.5658 250 2.64360147 2.087150864 0.789510404 80
 CETN2 centrin, EF-hand protein, 2 Hs.82794 -2.5116 893 -0.4096 673 2.106462937 1.613350432 0.76590497 177
 HYA22 HYA22 protein Hs.147189 -4.6575 239 -0.7082 70 2.299008086 1.780985556 0.774675638 124
 APG-1 heat shock protein (hsp110 family) Hs.71992 -3.3586 551 -0.4245 628 2.424332104 2.020451235 0.833405304 102
 Homo sapiens cDNA: FLJ21409 fis, clone COL03924 Hs.172129 -5.6737 130 -0.5131 366 3.676381159 3.215685679 0.874687781 24
 APLP2 amyloid beta (A4) precursor-like protein 2 Hs.279518 -5.486 145 -0.6434 131 2.60794139 2.232646111 0.856095202 82
 MDS001 x 001 protein Hs.35380 -1.4734 1518 -0.2508 1381 1.570364344 1.252326111 0.797474876 374
  **ESTs, Moderately similar to CLC3 HUMAN CHLORIDE CHANNEL PROTEIN 3 [H.sapiens] Hs.171553 -2.0422 1145 -0.3549 908 2.038995881 1.535755247 0.753191932 197
 ESTs, Moderately similar to CLC3 HUMAN CHLORIDE CHANNEL PROTEIN 3 [H.sapiens] Hs.171553 -1.7745 1305 -0.3118 1077 1.806623434 1.385288333 0.766783109 267
 TCEB1L transcription elongation factor B (SIII), polypeptide 1-like Hs.171626 -2.8337 754 -0.488 435 2.188651826 1.618121667 0.739323472 150
 Human DNA sequence from clone RP5-852M4 on chromosome 20  Hs.16475 -1.9124 1219 -0.326 1015 1.990495209 1.516318889 0.761779723 209
 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 Hs.6790 -3.3982 542 -0.5765 234 1.996766858 1.523171111 0.762818706 207
 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 Hs.6790 -2.7953 769 -0.5257 337 1.827085941 1.358873056 0.743737897 260
 RAB3A RAB3A, member RAS oncogene family Hs.27744 -2.1784 1063 -0.3618 875 1.683731684 1.342062222 0.797076063 316
 Homo sapiens mRNA; cDNA DKFZp564F093 (from clone DKFZp564F093) Hs.18724 -2.7894 771 -0.2626 1314 2.480922803 2.436835 0.982229272 98
 PLCB4 phospholipase C, beta 4 Hs.283006 -3.1012 651 -0.4519 527 2.380880321 2.328229438 0.97788596 326
 PLCB4 phospholipase C, beta 4 Hs.283006 -3.1053 648 -0.407 684 2.136851879 1.811691597 0.847832091 165
 PLCB4 phospholipase C, beta 4 Hs.283006 -4.8234 214 -0.4542 517 2.380880321 2.328229438 0.97788596 105
 EPB49 erythrocyte membrane protein band 4.9 (dematin) Hs.274122 -4.8825 205 -0.4451 548 2.781443649 2.688992191 0.966761341 61
 Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063 -5.2568 162 -0.4293 601 2.688731179 2.81833 1.048200736 74
 Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063 -6.5673 74 -0.5254 338 2.759070608 2.906431667 1.053409673 64
 ESTs Hs.13328 -5.1423 175 -0.441 558 2.771877918 2.791301667 1.007007433 62
 DKFZP564O0423 DKFZP564O0423 protein Hs.5028 -5.1578 173 -0.4371 568 2.684779787 2.752399444 1.025186296 76
 Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 Hs.193063 -5.2366 167 -0.4343 583 2.699885973 2.786557778 1.032102024 72
 KIAA1482 KIAA1482 protein Hs.278894 -3.1101 645 -0.4291 603 2.3199536 1.878432556 0.809685399 119
 Homo sapiens, Similar to hypothetical protein AB030201, clone MGC:3205, mRNA, complete cds Hs.43621 -3.6579 469 -0.6001 191 2.04442259 1.574938889 0.770358779 195
 KIAA1482 KIAA1482 protein Hs.278894 -3.2304 597 -0.5017 401 2.023030412 1.593345833 0.7876035 200
 ESTs Hs.23079 -6.835 60 -0.6123 175 3.214786479 2.9930875 0.931037728 36
 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 Hs.21330 -6.2286 88 -0.5991 195 3.205999863 2.8727875 0.896066008 37
 DNCI1 dynein, cytoplasmic, intermediate polypeptide 1 Hs.65248 -3.6093 486 -0.4229 633 2.632769103 2.250049198 0.85463218 81
 DNCI1 dynein, cytoplasmic, intermediate polypeptide 1 Hs.65248 -2.8685 737 -0.2875 1186 2.536382137 2.35443713 0.928265932 90
 SYNJ1 synaptojanin 1 Hs.127416 -2.6232 840 -0.5296 330 1.773732643 1.278777417 0.720952744 283