Supplementary Table 1 Genes up- and down- regulated in RMS (>1.5 fold and P-value < 0.001) 2851 genes up-regulated in rhabdomyosarcoma (>1.5 fold and P-value < 0.001) Accession # Sequence Name(s) P-value Fold Change AV168216 Zzz3,R75514,AA408566,AW556059,3110065C23Rik 1.88E-07 2.43009 BB379602 Zzef1,C85424,BC051585,MGC107545,mKIAA0399, 0.00009 2.30216 BB759260 Zyx,R75157,9530098H06Rik 3.93E-07 6.8602 BC013559 Zwint,Zwint-1,D10Ertd749e,2010007E07Rik,2600001N01Rik 4.02E-06 4.33115 BB420529 Zswim6,mKIAA1577,2900036G02Rik 1.28E-43 5.81057 BG072903 Zranb1,Gm1956,Trabid,D7Wsu87e,9330160G10Rik 0.00095 1.60955 NM_011769 Zim1 0.00009 3.83185 BB361162 Zic1,ZIC,ZNF201 1.83E-25 14.45411 NM_011764 Zfp90,NK10,Zfp64,Zfp83,KRAB17,mKIAA1954,6430515L01Rik 4.88E-07 3.30762 BM230481 Zfp82,mszf3,KRAB16,A030010D05 4.62E-10 3.57192 BC021921 Zfp709,HIT-40,BC021921,MGC28841 0.00019 1.85074 BB040500 Zfp647,Es492,6030449J21 7.06E-07 2.21975 NM_009564 Zfp64 0.00085 2.48661 AW548399 Zfp617,Zfps11-6 0.00091 2.17308 AV274175 Zfp608,MGC116601,4932417D18Rik 5.52E-07 2.78491 BE985246 Zfp59,Mfg2,Mfg-2 4.62E-06 1.6049 BM207314 Zfp568,C80731,Gm1691 0 4.817 BB150458 Zfp537,Tsh3,KIAA1474,mKIAA1474,A630038G13Rik 1.11E-09 4.39825 NM_013843 Zfp53,KRAZ1,zfas8,Zfp-53,Zfp118,D030067O06Rik 8.89E-06 2.04926 BM225280 Zfp52,Zfp76,KRAB11,Zfp-52,mszf24,mszf34,zfec29,mszf23-2 1.01E-07 2.90437 BG064695 Zfp482,ZID,ZBTB6,MGC41441,A830092L04Rik 0.0009 1.52711 BC023090 Zfp472,Krim1,KRIM-1,Krim-1A,Krim-1B 0.00018 1.82524 BB421061 Zfp451,COASTER,AI596398, 1.28E-06 3.17744 AK012846 Zfp444,FLJ00134,mFLJ00134,2810031J10Rik,6230401O10Rik 3.83E-07 2.73545 BM227942 Zfp422-rs1,AI842447,Krox-25-2,A430003O12Rik,C430039G02Rik 0.00076 1.80164 AW547438 Zfp407,Gm333,Gm334,Gm948,ZNF407,6430585N13Rik 4.33E-07 2.63122 NM_009554 Zfp37,Tzn,Zfp-37,AV042165 3.33E-07 3.48645 M58566 Zfp36l1,Brf1,ERF1,cMG1,Berg36,TIS11b, 2.95E-10 2.1344 BQ176698 Zfp369,NRIF2,B930030B22Rik,D230020H11Rik 7.51E-07 1.95403 AK014562 Zfp329,ZNF329,2810439M05Rik,4632409L22Rik 0.0001 2.37418 NM_018759 Zfp326,ZAN75,5730470H14Rik 0.00052 1.61594 BG075830 Zfp322a,RP23-9O13.9,9630054P07Rik 4.99E-12 1.53642 NM_013889 Zfp292,Zn-15,Zn-16 0.00032 1.64396 BE651907 Zfp286,BC027023,MGC39058,RP23-59B16.5 0.00003 5.01023 L36316 Zfp260,Ozrf1,Zfp63,AI480997 0.00073 1.80779 AV346442 Zfp26,Zfp70,mkr-3,KRAB15,Zfp-26,mszf14,mszf52 3.62E-16 1.70624 X98096 Zfp148,BERF-1,BFCOL1,ZBP-89,AI480666,AW045217 2.69E-08 1.8039 BB154236 Zfp142,BB154236,mKIAA0236,9330177B18Rik 1.37E-06 2.5965 AV263718 Zfp110,NRIF,Nrif1,N28112,2900024E01Rik 0.00082 1.53557 NM_009544 Zfp105,AW557864 1.22E-09 2.9553 NM_015753 Zfhx1b,SIP1,Zfx1b,Zfxh1b,mKIAA0569,9130203F04Rik 3.76E-20 3.88171 AV363000 Zfhx1a,BZP,ZEB,MEB1,Nil2,Tcf8,AREB6,Tcf18,Zfhep, 4.15E-08 2.86147 NM_133349 Zfand2a,Airap,AA407930,AU016206 5.35E-08 2.97538 BB271151 Zdhhc24,Leng4,5730496N17Rik 0.00036 2.24875 BC019536 Zdhhc20,AI448102,5033406L14Rik,B230110O18Rik 2.16E-16 4.27936 AV361868 Zdhhc14,New1cp,MGC29194,B530001K09Rik 0.00012 2.25267 AK010382 Zdhhc13,HIP3RP,Hip14l,C530010M18,2410004E01Rik 1.44E-07 2.09971 AV140894 Zcchc3,2810406K24Rik 0.00087 2.45231 BB223737 Zcchc14,BDG29,AA792890,KIAA0579 3.32E-08 5.64842 AW556219 Zc3h7a,Zc3h7,HSPC055,Zc3hdc7,AI447294,AW556219, 0.00024 1.7232 BG922355 Zbtb36,B230208J24Rik 4.78E-18 7.6601 AV027921 Ywhaz,AI596267,AL022924,AU020854,1110013I11Rik 9.65E-06 3.67075 AV024540 Ywhaq,R74690,AA409740,AU021156,MGC118161 0.00035 1.97938 NM_018753 Ywhab,14-3-3 beta,1300003C17Rik 0.00013 2.04605 BC009080 Yipf1,C030002N13Rik 3.05E-06 1.9655 BG070675 Yap1,Yap,65kDa,YAP65,AI325207 0.00001 6.01672 NM_011917 Xrn2 4.91E-09 2.12406 BG064541 Xpo4,mKIAA1721,B430309A01Rik 0.00082 1.57655 BC005560 Xlr 0.00014 2.56382 AV051768 Xbp1,TREB5,XBP-1,TREB-5,D11Ertd39e 5.24E-11 1.82847 BC014727 Wwtr1,TAZ,C78399,2310058J06Rik,2610021I22Rik 7.93E-06 2.88043 AK004087 Wwp2,AIP2,AA690238,AW554328,1300010O06Rik 0.00018 5.91992 BE136550 Wtip 3.30E-18 3.38288 BM730566 Wsb2,Swip2,WSB-2,AA673511 3.25E-06 3.1205 BC019601 Wsb1,1110056B13Rik,2700038M07Rik 2.82E-13 3.61184 NM_030215 Wrnip1,WHIP,Wrnip,4833444L21Rik 2.24E-23 3.93178 NM_009525 Wnt5b,Wnt-5b,AW545702 7.53E-06 5.94733 BC018425 Wnt5a,Wnt-5a,8030457G12Rik 0 6.32702 BI692255 Wnk1,Prkwnk1,mKIAA0344,6430573H23Rik 3.82E-06 1.7165 NM_018865 Wisp1,Elm1,AW146261 3.27E-31 29.54223 BI251603 Wipi1,AW411817,MGC36416,D11Ertd498e,4930533H01Rik 9.62E-07 1.97502 BI658695 Whsc1l1,NSD3,AI528490,A530023P05 0.00089 3.36446 BQ177743 Whsc1,Whsc1l,AW555663,mKIAA1090 9.71E-06 3.51548 NM_134139 Wdr74,AA407588,5730436H21Rik 0.00062 1.57214 AK002371 Wdr57,Prp8bp,0610009C03Rik 0.00006 1.71756 AI415371 Wdr19,PWDMP,mKIAA1638,C330027H04Rik,D330023L08Rik 0.00005 2.71503 AW542545 Wdr1,D5Wsu185e 6.78E-06 2.19091 NM_024479 Wbscr27,MGC8159,AW492986,BC002286 0.00064 3.08605 BC007478 Wbp5,AL024233 4.04E-16 2.48701 NM_031877 Wasf1,Scar,WAVE,WAVE-1,AI195380,AI838537 0.00013 2.33276 BM240052 Vps41,Vam2,mVam2,AI317346 0.00049 1.57065 NM_030559 Vps16,MGC7352,1810074M16Rik 0.00018 1.78868 AK003237 Vkorc1,D7Wsu86e 0.00028 1.81507 M24849 Vim,MGC102095 7.03E-35 3.33062 BM119387 Vil2,p81,ezrin,R75297,AW146364,MGC107499,cytovillin 4.76E-08 3.1633 NM_009502 Vcl,AA571387,AI462105,AW545629,9430097D22 4.53E-07 1.6678 BB250384 Vcam1,CD106,Vcam-1 4.16E-08 4.4065 BB742957 Uty,Hydb,KIAA4057,mKIAA4057 0 36.36382 BB153362 Utrn,DRP,Dmdl,AA589569 0.00003 8.13706 AW107303 Usp9x,Fafl,Dffrx,FAF-X,AA407302,AA407699,AL022658, 8.09E-31 2.13824 AB045709 Usp8,Ubpy,AI574262,AW557536,mKIAA0055 0.00028 1.53355 BM233265 Usp3,AA409661,BC017156,MGC28886 0.00009 1.96204 AI427806 Usp22,AI427806,KIAA1063,MGC91200,mKIAA1063,9330200A01 0.00017 1.76249 AK006800 Usp20,Vdu2,AI467231,1700055M05Rik 7.51E-08 5.67967 AW539189 Usp12,Ubh1 0.00027 2.63202 AI117611 Usp11,MGC6649,KIAA4085,mKIAA4085,6230415D12Rik 1.10E-13 3.57519 BC018179 Usp1,MGC25559 4.70E-07 2.34283 NM_009477 Upp1,Up,Upp,UPase,UdRPase,AI325217 6.14E-36 11.01495 BB219662 Upk1b,UPIb,Upk1,Tspan20,AI413235 3.16E-27 20.3888 BM226250 Unc5c,rcm,Unc5h3,AI047720,6030473H24,B130051O18Rik 0.00037 6.51702 BG065285 Unc5b,Unc5h2,A630020F16,D10Bwg0792e,6330415E02Rik 7.58E-15 8.88249 BB464342 Unc45a,AW538196 0.00016 4.8632 BQ266387 Uhrf2,Nirf,AI426270,AW214556,2310065A22Rik,D130071B19Rik 0.00019 2.08508 NM_053184 Ugt2a1 0.00024 3.36764 NM_009466 Ugdh,Udpgdh 6.18E-06 2.39509 BM211361 Ugcgl1,AA589501,AI414429,AI448372,0910001L17Rik 1.15E-20 2.25635 AA591863 Ugcg,Ugcgl,C80537,Epcs21,GlcT-1,AU043821 2.62E-09 6.95918 NM_026435 Ufm1,AI132708,AI463323,1810045K17Rik 0.00012 2.30698 AW108044 Ucp2,Slc25a8 0.00046 1.83128 NM_030724 Uck2,UK,UMK,Umpk,TSA903,AA407809,AI481316 0.00006 4.12208 NM_011670 Uchl1,gad,C88048,PGP9.5,R75593,AW822034 8.56E-38 6.9241 BB253461 Ubxd2,KIAA0242,mKIAA0242,1300013G12Rik 1.12E-10 6.49582 BC016129 Ubtd1,BC016129,MGC28905 0.00008 4.05438 NM_013699 Ubp1,Cp2b,NF2d9,LBP-1a,LBP-1b 8.04E-07 1.90585 AK016093 Ube4b,UFD2,UFD2a,Ufd2p, 0.00043 4.89101 BB796558 Ube2w,6130401J04Rik 9.19E-40 2.88704 BF472749 Ube2j1,Ncube,Ubc6p,Ncube1,0710008M05Rik,1110030I22Rik 0.00001 1.80343 BM242612 Ube2i,UBC9,Ubce9,Mmubc9,Ubce2i,5830467E05Rik 6.64E-08 3.08933 BI438002 Ube1dc1,AW240750,5730525G14Rik 0.0002 1.78572 AI482041 Ubap2l,C77168,Nice-4, 0.00041 4.46128 BG963358 Uap1l1,5730445F03Rik 2.53E-07 2.50763 AW542140 U2af1-rs2,35kDa,C77286,5031411E02Rik,A230052C13Rik 0.00011 2.24527 NM_024187 U2af1,35kDa,2010107D16Rik 0.00041 1.5122 BC020139 Tyms,TS 0.00005 3.35804 AK004219 Txnl5,TRP14,D11Ertd672e,4831443O22Rik,RP23-207N15.4 0.00003 1.58279 NM_025299 Txnl4,Dim1,U5-15kD,U5-15kDa 0.00002 4.28416 NM_025334 Txndc12,ERp19,0610040B21Rik 5.38E-08 1.79225 NM_011660 Txn1,ADF,Txn,AW550880 4.79E-26 1.77416 BG070463 Txlna,Txln,AI425952,AW209241,MGC77972,MGC86145, 6.81E-07 6.66388 BC004850 Twsg1,Tsg,Twg,AW552143,D17Ertd403e,1810013J15Rik 3.81E-12 4.8169 NM_030254 Tusc3,N33,MGC6989,AU022242,BC003311 0.00019 1.90576 BB667130 Tulp4,Tusp,1110057P05Rik 1.70E-20 4.77645 BQ178976 Tubgcp2,1700022B05Rik 2.62E-06 3.82656 NM_026473 Tubb6,BB220206,2310057H16Rik 0 7.88058 NM_011655 Tubb5,AA408537,AI596182,M(beta)5,B130022C14Rik 6.79E-41 5.16786 AA986082 Tubb2b,2410129E14Rik 4.04E-14 8.24627 BC003475 Tubb2a,Tubb2,M(beta)2 2.68E-15 4.59273 NM_009448 Tuba6,M[a]6 0.00008 2.02814 NM_009446 Tuba3,M[a]3,AI528779,MGC107295 8.04E-32 22.61037 BC008117 Tuba2,MGC102558,MGC117866,MGC118411 1.11E-19 2.83886 NM_011653 Tuba1,Tuba-1,MGC102097,MGC102098,MGC102099 8.74E-11 2.8343 AK016145 Ttll5,R75373,AI428864,mKIAA0998,1700048H13Rik 2.19E-11 10.05176 BB764137 Ttll1,AV014541,6330444E16Rik 0.00001 3.52484 BC018513 Ttl,2410003M22Rik 2.05E-08 2.57546 BB106428 Ttc9,AI429215,AI853559,1700029M07Rik 0 10.59357 BC017523 Ttc8,BBS8,AV001447,0610012F22Rik 2.35E-07 2.62042 BM116591 Ttc3,TPRD,AA409221,D16Ium21,KIAA4119 0.00008 2.60245 BM238672 Ttc14,cI-44,AI662468,AU014779,AW561908, 1.48E-09 1.91907 AV332105 Tspyl5,6330530B20,E130308C19Rik 0.0006 2.31038 AK020159 Tspan9,AU018597,6720474K14Rik,9430079M16Rik 4.13E-07 3.07294 NM_019656 Tspan6,T245,Tm4sf,Tm4sf6,TSPAN-6,AI316786 2.41E-21 5.47364 NM_019571 Tspan5,NET-4,Tm4sf9,AU024142,2810455A09Rik,4930505M03Rik 0.00025 2.81191 NM_053082 Tspan4,NAG-2,Tm4sf7,Tspan-4,AI325509,AI746565 1.47E-07 3.15741 AU016382 Tsc22d1,TSC,Egr5,TSC-22,Tgfb1i4,AA589566,AW105905 0 2.97769 NM_133901 Trrap,AI481500 4.21E-06 1.66403 BB360644 Trps1,AI115454,AI447310,MGC46754,MGC107472,D15Ertd586e 1.39E-08 2.07727 BB377721 Trpm3,MLSN2,LTRPC3,AU018608,9330180E14, 2.68E-06 4.46255 NM_013838 Trpc6,Trrp6,mtrp6,AV025995,LLHWJM002,LLHWJM003 3.15E-12 8.89173 BB817939 Trpc1,Trrp1 5.72E-07 6.41965 BB309395 Trpa1,Anktm1 0 100 AF075434 Trp63,Ket,p63,Tp63,p73L,TAp63,p51/p63,AI462811,