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Statistics of Affymetrix and Custom CDF Files (Version 10)

Table 1: Probe utilization
SpeciesChipProbe countUG (%)REFSEQ (%)ENTREZG (%)ENSG (%)ENST (%)ENSE (%)VEGAG (%)VEGAT (%)VEGAE (%)TAIR (%)
Arabidopsis thalianaAtGenome130858NA89.2NANANANANANANA89.3
Arabidopsis thalianaAtH1250103NA90.3NANANANANANANA90.7
Arabidopsis thalianaArabidopsis Tiling 1.0R Array3130523NA15.7NANANANANANANA15.8
Bos taurusBovine26412658.350.443.931.135.927NANANANA
Canis familiarisCfCanine247165038.62.350.846.653.238.9NA.1NANA
Drosophila melanogasterDmDrosophila22627667676.5NA73.476.472.3NANANANA
Drosophila melanogasterDmGenome119518692.993.3NA92.493.290.6NANANANA
Danio rerioDrZebrafish24801354.456.739.634.638.632.4NA26.9NANA
Gallus gallusGgChicken42282552.91443.13843.432.1NANANANA
Homo sapiensHs133A24679968.572.467.56871.263.366.771.362.7NA
Homo sapiensHs133Av224679968.572.467.56871.263.366.771.362.7NA
Homo sapiensHs133B24833653.534.530.73334.231.438.340.736.7NA
Homo sapiensHs133P60315857.548.344.54648.143.249.45346.9NA
Homo sapiensHs133X67280455.146.343.244.645.943.748.451.347.6NA
Homo sapiensHs95Av21976957175.170.270.573.668.568.873.167NA
Homo sapiensHsEx10stv2538365428.22221.621.821.521.623.724.423.5NA
Homo sapiensHsFocus9734976.484.979.678.582.172.275.280.169.7NA
Homo sapiensHsNuGOHs1a5201802644076969.965.669.772.665.765.669.662.2NA
Homo sapiensChromosome 21/22 1.0 Array Set A3336921.4.6.6.5.5.51.21.21.1NA
Homo sapiensChromosome 21/22 1.0 Array Set B3336655.22.52.62.82.82.54.54.54.2NA
Homo sapiensChromosome 21/22 1.0 Array Set C3343615.22.82.7332.73.63.73.3NA
Homo sapiensChromosome 21/22 2.0R Array22432014.32.42.32.22.22.23.33.33.3NA
Homo sapiensENCODE 2.0R Array22142805.43.333.23.23.25.15.15.1NA
Homo sapiensHuman Promoter 1.0R Array435620795.14.94.84.94.55.75.95.4NA
Homo sapiensHuman Tiling 1.0R Array Set 0131049804.12.122.32.42.23.23.23NA
Homo sapiensHuman Tiling 1.0R Array Set 0231049562.91.31.31.21.21.1.91.8NA
Homo sapiensHuman Tiling 1.0R Array Set 0331049593.31.61.51.41.41.31.71.71.6NA
Homo sapiensHuman Tiling 1.0R Array Set 0431049682.51.21.111.9.8.9.8NA
Homo sapiensHuman Tiling 1.0R Array Set 0531049922.71.21.11.11.11.9.9.8NA
Homo sapiensHuman Tiling 1.0R Array Set 0631049623.21.51.41.51.51.41.921.7NA
Homo sapiensHuman Tiling 1.0R Array Set 0731049692.71.31.21.21.21.11.41.71.3NA
Homo sapiensHuman Tiling 1.0R Array Set 0831050073.11.51.41.61.61.52.12.12NA
Homo sapiensHuman Tiling 1.0R Array Set 0931049923.71.81.81.81.81.71.21.31.1NA
Homo sapiensHuman Tiling 1.0R Array Set 1031049923.21.61.51.51.51.3221.8NA
Homo sapiensHuman Tiling 1.0R Array Set 1131049643.81.91.81.71.71.52.42.42.2NA
Homo sapiensHuman Tiling 1.0R Array Set 1231049664.12.22.1221.82.82.92.6NA
Homo sapiensHuman Tiling 1.0R Array Set 1331049574.52.72.62.62.62.43.53.53.2NA
Homo sapiensHuman Tiling 1.0R Array Set 1414874402.21.51.41.51.51.42.22.22.1NA
Homo sapiensHuman Tiling 2.0R Array Set 0160209613.71.91.8221.82.72.72.5NA
Homo sapiensHuman Tiling 2.0R Array Set 0261903293.721.91.91.91.71.921.8NA
Homo sapiensHuman Tiling 2.0R Array Set 0361091143.11.61.61.51.51.42.22.22NA
Homo sapiensHuman Tiling 2.0R Array Set 0461991622.91.41.31.31.31.21.51.51.4NA
Homo sapiensHuman Tiling 2.0R Array Set 0562511183.11.51.41.41.41.21.41.71.3NA
Homo sapiensHuman Tiling 2.0R Array Set 0661240673.51.81.71.61.71.51.61.71.5NA
Homo sapiensHuman Tiling 2.0R Array Set 0760906393.61.81.81.81.81.62.52.52.3NA
Macaca mulattaRhesus66718617.5.648.236.337.134.4NANANANA
Mus musculusMm11KsubA13018062.964.360.856.158.55530.431.629.9NA
Mus musculusMm11KsubB11848049.251.846.344.749.843.122.725.122NA
Mus musculusMm43049537460.252.348.945.948.542.827.228.525.9NA
Mus musculusMm430A24886472.973.368.865.169.260.335.237.233.2NA
Mus musculusMouse Genome 430A 2.024886472.973.368.865.169.260.335.237.233.2NA
Mus musculusMm430B24761047.431.22926.527.725.119.119.718.5NA
Mus musculusMm74Av120064156.256.352.849.352.447.526.427.825.7NA
Mus musculusMm74Av219667062.664.160.256.159.654.230.231.929.5NA
Mus musculusMm74Bv219580861.151.748.944.746.643.627.728.627.3NA
Mus musculusMm74Cv218147434.220.819.917.718.217.412.612.912.5NA
Mus musculusMmEx10stv1473763427.922.42221.221.320.9131312.9NA
Mus musculusMmNuGOMm1a52017726163565.46460.258.561.954.230.53228.7NA
Mus musculusMouse Promoter 1.0R Array43696367.95.14.94.44.54.13.13.12.9NA
Mus musculusMouse Tiling 1.1R Array Set 0130769262.91.71.61.41.41.3.9.9.8NA
Mus musculusMouse Tiling 1.1R Array Set 0231616333.62.12.11.921.8332.8NA
Mus musculusMouse Tiling 1.1R Array Set 0325348032.71.51.51.41.41.3.8.8.8NA
Mus musculusMouse Tiling 1.1R Array Set 0425655193.21.91.91.81.81.62.62.62.5NA
Mus musculusMouse Tiling 1.1R Array Set 0531531761.81.81.311.2.91.41.41.3NA
Mus musculusMouse Tiling 1.1R Array Set 0631662012.81.61.61.41.41.31.11.11NA
Mus musculusMouse Tiling 1.1R Array Set 0731231893.92.52.42.22.2211.9NA
Mus musculusMouse Tiling 1.1R Array Set 0830501302.71.41.41.31.31.1.4.4.4NA
Mus musculusMouse Tiling 1.1R Array Set 0931556913.11.81.71.51.51.4.4.4.4NA
Mus musculusMouse Tiling 1.1R Array Set 1030480633.11.81.81.61.61.4.6.6.5NA
Mus musculusMouse Tiling 1.1R Array Set 1131672003.92.42.32.22.222.62.62.4NA
Mus musculusMouse Tiling 1.1R Array Set 1231658433.42.121.81.81.6.5.5.5NA
Mus musculusMouse Tiling 1.1R Array Set 1330831842.71.51.41.31.31.2.7.7.6NA
Mus musculusMouse Tiling 1.1R Array Set 1431464173.21.91.81.61.61.511.9NA
Mus musculusMouse Tiling 2.0R Array Set 0158883943.31.91.81.61.61.5.6.6.6NA
Mus musculusMouse Tiling 2.0R Array Set 0260989812.61.91.71.41.51.32.22.22.1NA
Mus musculusMouse Tiling 2.0R Array Set 03588359831.81.71.61.61.5.8.8.7NA
Mus musculusMouse Tiling 2.0R Array Set 0458657233.62.22.22.12.11.92.52.52.3NA
Mus musculusMouse Tiling 2.0R Array Set 0557924982.91.71.71.51.51.3.6.7.6NA
Mus musculusMouse Tiling 2.0R Array Set 0658884782.91.61.51.41.41.3.8.8.8NA
Mus musculusMouse Tiling 2.0R Array Set 0756695072.71.61.51.41.41.2.5.5.4NA
Oryza sativaOsRice629427NA45.8NANANANANANANANA
Pan troglodytesHs133A246799NA72.849.54649.641.5NANANANA
Pan troglodytesHs133Av2246799NA72.849.54649.641.5NANANANA
Pan troglodytesHs133B248336NA33.227.620.621.918.9NANANANA
Pan troglodytesHs133P603158NA47.73530.332.627.5NANANANA
Pan troglodytesHs133X672804NA45.733.728.630.327.7NANANANA
Pan troglodytesHs95Av2197695NA75.652.44851.346NANANANA
Pan troglodytesHsEx10stv25383654NA2118.616.216.415.4NANANANA
Pan troglodytesHsFocus97349NA85.655.75357.147NANANANA
Pan troglodytesHsNuGOHs1a520180264407NA68.348.544.547.840.5NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set A333692NA.6.6.4.4.4NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set B333665NA2.52.41.81.81.5NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set C334361NA2.82.2221.7NANANANA
Pan troglodytesChromosome 21/22 2.0R Array2243201NA2.31.91.51.61.5NANANANA
Pan troglodytesENCODE 2.0R Array2214280NA3.32.72.12.12.1NANANANA
Pan troglodytesHuman Promoter 1.0R Array4356207NA4.74.63.23.32.9NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 013104980NA21.91.51.51.3NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 023104956NA1.31.3.91.8NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 033104959NA1.51.41.11.1.9NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 043104968NA1.11.1.8.8.7NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 053104992NA1.11.1.8.8.7NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 063104962NA1.41.311.1.9NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 073104969NA1.31.3.9.9.8NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 083105007NA1.51.411.1.9NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 093104992NA1.71.71.21.31.1NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 103104992NA1.51.51.11.1.9NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 113104964NA1.81.71.31.41.2NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 123104966NA2.121.51.51.3NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 133104957NA2.62.11.71.71.4NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 141487440NA1.51.2.8.8.7NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 016020961NA1.81.71.31.31.1NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 026190329NA1.91.71.31.31.1NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 036109114NA1.61.411.1.9NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 046199162NA1.31.311.8NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 056251118NA1.51.411.9NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 066124067NA1.71.61.21.21NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 076090639NA1.71.71.21.31.1NANANANA
Rattus norvegicusRn23034145964.545.940.331.833.828.6NANANANA
Rattus norvegicusRn230A17452669.760.553.64446.739.4NANANANA
Rattus norvegicusRn230B16803359.230.826.619.120.317.5NANANANA
Rattus norvegicusRn34A13913764.663.554.648.952.846.3NANANANA
Rattus norvegicusRnEx10stv1402777623.522.821.521.621.621.3NANANANA

Table 2. Target Count for Affymetrix and Custom Probe Sets
SpeciesChipAffy-UG1Affy-ENSG2Affy-REFSEQ3UGREFSEQENTREZGENSGENSTENSEVEGAGVEGATVEGAETAIR
Arabidopsis thalianaAtGenome1281NA7336NA8940NANANANANANANA7214
Arabidopsis thalianaAtH1NANA21684NA25254NANANANANANANA21025
Arabidopsis thalianaArabidopsis Tiling 1.0R ArrayNANANANA15565NANANANANANANA13400
Bos taurusBovine163065260103731192011289942874931024511245NANANANA
Canis familiarisCfCanine21554216612170021296977515771165042192231933NA58NANA
Drosophila melanogasterDmDrosophila2NA13636136481349019293NA134131909920479NANANANA
Drosophila melanogasterDmGenome1NA12169122081209117582NA121031737720475NANANANA
Danio rerioDrZebrafish124595458857589221158769436071826510092NA5264NANA
Gallus gallusGgChicken17149121721230916872395412495119981653023711NANANANA
Homo sapiensHs133A131031198413280118451753111961118342374022299131253400029156NA
Homo sapiensHs133Av2130421198413280118451753111961118342374022299131253400029156NA
Homo sapiensHs133B1521764311049210843872960796290113501070979041715615040NA
Homo sapiensHs133P295841732220483221822500417527172153397734541200835101047113NA
Homo sapiensHs133X294751735320609218042475517386170313293931612199284851642941NA
Homo sapiensHs95Av278638297907781591226081358065159961484489292239519335NA
Homo sapiensHsEx10stv2NANANA52928352432385126116416242327053083984754315922NA
Homo sapiensHsFocus80687764849474841153078157676147511201585332071115301NA
Homo sapiensHsNuGOHs1a520180NANANA166502266916242171582982025957180333930531280NA
Homo sapiensChromosome 21/22 1.0 Array Set ANANANA26668483970171111258475NA
Homo sapiensChromosome 21/22 1.0 Array Set BNANANA5562602321893258864259271792NA
Homo sapiensChromosome 21/22 1.0 Array Set CNANANA5292501651772939052564281123NA
Homo sapiensChromosome 21/22 2.0R ArrayNANANA1527669445438688335875616605707NA
Homo sapiensENCODE 2.0R ArrayNANANA832371239242625270945819776200NA
Homo sapiensHuman Promoter 1.0R ArrayNANANA1615713943955992071716624131106842746235177NA
Homo sapiensHuman Tiling 1.0R Array Set 01NANANA375417141125999264586021744570313864NA
Homo sapiensHuman Tiling 1.0R Array Set 02NANANA307699766659599641174358092949NA
Homo sapiensHuman Tiling 1.0R Array Set 03NANANA325210967266251056481480921956701NA
Homo sapiensHuman Tiling 1.0R Array Set 04NANANA276689160250583533803788662746NA
Homo sapiensHuman Tiling 1.0R Array Set 05NANANA312993561951894634733787292466NA
Homo sapiensHuman Tiling 1.0R Array Set 06NANANA3271124481572819185531132343437044NA
Homo sapiensHuman Tiling 1.0R Array Set 07NANANA3106114968360510043633108927875210NA
Homo sapiensHuman Tiling 1.0R Array Set 08NANANA3197116977373717985593123433907991NA
Homo sapiensHuman Tiling 1.0R Array Set 09NANANA3636155810339711787609667621814974NA
Homo sapiensHuman Tiling 1.0R Array Set 10NANANA3175120082172312325059110731137729NA
Homo sapiensHuman Tiling 1.0R Array Set 11NANANA371614641072898142959631658405912018NA
Homo sapiensHuman Tiling 1.0R Array Set 12NANANA3986181012201075166969731865539314763NA
Homo sapiensHuman Tiling 1.0R Array Set 13NANANA4277221815321505267986842228541212744NA
Homo sapiensHuman Tiling 1.0R Array Set 14NANANA998642397356866250173717623875NA
Homo sapiensHuman Tiling 2.0R Array Set 01NANANA697830052015178947611441231281029021608NA
Homo sapiensHuman Tiling 2.0R Array Set 02NANANA71543066215120213685129842168551313814NA
Homo sapiensHuman Tiling 2.0R Array Set 03NANANA60532617170215462932101202599676216548NA
Homo sapiensHuman Tiling 2.0R Array Set 04NANANA6282228615111336245489711816476212884NA
Homo sapiensHuman Tiling 2.0R Array Set 05NANANA6693262316921508249692751987468911305NA
Homo sapiensHuman Tiling 2.0R Array Set 06NANANA68672912192917962897106361666549912457NA
Homo sapiensHuman Tiling 2.0R Array Set 07NANANA70782945204417823411117253248949422674NA
Macaca mulattaRhesusNANANA593132216002139252394029321NANANANA
Mus musculusMm11KsubA214941375186436656754255399451596049212748364875NA
Mus musculusMm11KsubB253230633544276837652833276537095486136739784520NA
Mus musculusMm43023598157262050019444215611647515768210372543879212017420657NA
Mus musculusMm430A13395118851356812370155341217511723157181876557471503614936NA
Mus musculusMouse Genome 430A 2.013395118851356812370155341217511723157181876557471503614936NA
Mus musculusMm430B13060549411325932779175716540068787688342568456737NA
Mus musculusMm74Av18199696488877318902670046676870710239338380108045NA
Mus musculusMm74Av28198771290597786998177377374962111323375389218961NA
Mus musculusMm74Bv2870155627818700172335645529568357899300366776626NA
Mus musculusMm74Cv2684035196391450237382721245430843102164431142878NA
Mus musculusMmEx10stv1NANANA38321352322444422927302111987571290640421162329NA
Mus musculusMmNuGOMm1a520177NANANA16349200911541515297188662007775801558114472NA
Mus musculusMouse Promoter 1.0R ArrayNANANA138921422598819739124822100950091356019411NA
Mus musculusMouse Tiling 1.1R Array Set 01NANANA223012668618331082472333511773169NA
Mus musculusMouse Tiling 1.1R Array Set 02NANANA2731165012131201168966091561453211833NA
Mus musculusMouse Tiling 1.1R Array Set 03NANANA19361087760725907356329111022478NA
Mus musculusMouse Tiling 1.1R Array Set 04NANANA2063132291690012425023118732868362NA
Mus musculusMouse Tiling 1.1R Array Set 05NANANA1675284412809291328337298121934660NA
Mus musculusMouse Tiling 1.1R Array Set 06NANANA24891471106010011262477252516964295NA
Mus musculusMouse Tiling 1.1R Array Set 07NANANA31822309165715781970752150118064447NA
Mus musculusMouse Tiling 1.1R Array Set 08NANANA22001180836842103944032067271810NA
Mus musculusMouse Tiling 1.1R Array Set 09NANANA24881391985980122851871726621744NA
Mus musculusMouse Tiling 1.1R Array Set 10NANANA2479142010271001125555592118892408NA
Mus musculusMouse Tiling 1.1R Array Set 11NANANA3086187513651331191581071361383010615NA
Mus musculusMouse Tiling 1.1R Array Set 12NANANA2718178512281198153463132368612131NA
Mus musculusMouse Tiling 1.1R Array Set 13NANANA22471219855839104742622669642521NA
Mus musculusMouse Tiling 1.1R Array Set 14NANANA26261591112910911406565240916934307NA
Mus musculusMouse Tiling 2.0R Array Set 01NANANA475827231906186223671039243715444344NA
Mus musculusMouse Tiling 2.0R Array Set 02NANANA4091429323441975281993052457638815802NA
Mus musculusMouse Tiling 2.0R Array Set 03NANANA47813064215620532556982270425526205NA
Mus musculusMouse Tiling 2.0R Array Set 04NANANA52723428240923443308137752507692218635NA
Mus musculusMouse Tiling 2.0R Array Set 05NANANA44042591181017692258931149820175224NA
Mus musculusMouse Tiling 2.0R Array Set 06NANANA45132556182017672197901263423326337NA
Mus musculusMouse Tiling 2.0R Array Set 07NANANA41172352167615942010871442613123390NA
Oryza sativaOsRice23634NA2339NA24015NANANANANANANANA
Pan troglodytesHs133ANANANANA1760310628102131671016213NANANANA
Pan troglodytesHs133Av2NANANANA1760310628102131671016213NANANANA
Pan troglodytesHs133BNANANANA79066328507775817307NANANANA
Pan troglodytesHs133PNANANANA2394415906148622402424863NANANANA
Pan troglodytesHs133XNANANANA2369515549143622286023135NANANANA
Pan troglodytesHs95Av2NANANANA12400730768691096511029NANANANA
Pan troglodytesHsEx10stv2NANANANA25954246752045731837175435NANANANA
Pan troglodytesHsFocusNANANANA118276716648999648515NANANANA
Pan troglodytesHsNuGOHs1a520180NANANANA2154214715140502038218112NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set ANANANANA52524166152NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set BNANANANA249211143253703NANANANA
Pan troglodytesChromosome 21/22 1.0 Array Set CNANANANA229172166260665NANANANA
Pan troglodytesChromosome 21/22 2.0R ArrayNANANANA6135204296852996NANANANA
Pan troglodytesENCODE 2.0R ArrayNANANANA3583092384142047NANANANA
Pan troglodytesHuman Promoter 1.0R ArrayNANANANA11797967278761226816748NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 01NANANANA1327127096918685903NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 02NANANANA7257675668553340NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 03NANANANA7948276009653941NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 04NANANANA6276864867242632NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 05NANANANA6697375047632721NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 06NANANANA90891066612153832NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 07NANANANA8808935899413040NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 08NANANANA96094566513273741NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 09NANANANA1212118587114884551NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 10NANANANA91089267411244093NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 11NANANANA1123111283212974969NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 12NANANANA13661384104115945536NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 13NANANANA19941709143022696140NANANANA
Pan troglodytesHuman Tiling 1.0R Array Set 14NANANANA6335273355611437NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 01NANANANA22812234168731689845NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 02NANANANA25072426190830539549NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 03NANANANA22321997146823847463NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 04NANANANA17191753127420136972NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 05NANANANA19572006145122287320NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 06NANANANA23102206166126028564NANANANA
Pan troglodytesHuman Tiling 2.0R Array Set 07NANANANA22502176160627638805NANANANA
Rattus norvegicusRn23023331940514279186411867011498100341343914339NANANANA
Rattus norvegicusRn230A129827102104901087313167861975431006710248NANANANA
Rattus norvegicusRn230B1216231436852906875493923322642294470NANANANA
Rattus norvegicusRn34A505039945205467657444224393557187469NANANANA
Rattus norvegicusRnEx10stv1NANANA3140636595212802190131601192279NANANANA

Table 3. Affy vs Custom
CdfSpeciesChipAffy OnlyCustom OnlySharedPercentage of
identical probesets
in shared targets
Percentage of
probesets with
difference<=25%
in shared targets
Percentage of
probesets with
difference>50%
in all targets
ENSGBos taurusBovine1198343140622071.256.7
ENSGCanis familiarisCfCanine210869781552618.278.515.5
ENSGDrosophila melanogasterDmDrosophila2287641334966.799.12.7
ENSGDrosophila melanogasterDmGenome11741081199592.599.12.5
ENSGDanio rerioDrZebrafish15422155391618.181.950.8
ENSGGallus gallusGgChicken118410101098820.777.820.1
ENSGHomo sapiensHs133A6785281130642.191.211.4
ENSGHomo sapiensHs133Av26785281130642.191.211.4
ENSGHomo sapiensHs133B525384590650.691.214.6
ENSGHomo sapiensHs133P970863163523990.411.8
ENSGHomo sapiensHs133X11127901624149.790.612.2
ENSGHomo sapiensHs95Av2528296776948.39111.5
ENSGHomo sapiensHsFocus430342733450.293.510.6
ENSGMus musculusMm11KsubA322179381539.68814.8
ENSGMus musculusMm11KsubB446148261719.875.225.4
ENSGMus musculusMm4308669081486040.689.412.3
ENSGMus musculusMm430A7165541116941.490.711.9
ENSGMus musculusMouse Genome 430A 2.07165541116941.490.711.9
ENSGMus musculusMm430B547453494751.690.118.3
ENSGMus musculusMm74Av1679391628543.188.217.2
ENSGMus musculusMm74Av2748410696438.380.818
ENSGMus musculusMm74Bv2527260503544.986.516.6
ENSGMus musculusMm74Cv21241176227837.370.344.7
ENSGRattus norvegicusRn2307531382865235.386.422.1
ENSGRattus norvegicusRn230A507948659540.390.319.7
ENSGRattus norvegicusRn230B473556267034.283.330.5
ENSGRattus norvegicusRn34A346287364822.78318.2
ENTREZGBos taurusBovine27371157827130.373.137.1
ENTREZGCanis familiarisCfCanine214261901558117.774.314.1
ENTREZGDanio rerioDrZebrafish53672165477816.975.964.7
ENTREZGGallus gallusGgChicken161217921070319.466.530.3
ENTREZGHomo sapiensHs133A17072441171737.882.317.6
ENTREZGHomo sapiensHs133Av217072441171737.882.317.6
ENTREZGHomo sapiensHs133B481221158683565.551.5
ENTREZGHomo sapiensHs133P37974171711025.260.729.7
ENTREZGHomo sapiensHs133X40914491693732.662.530.6
ENTREZGHomo sapiensHs95Av21175171796444.883.818
ENTREZGHomo sapiensHsFocus825132768349.792.312.3
ENTREZGMus musculusMm11KsubA1245126412938.884.629.2
ENTREZGMus musculusMm11KsubB858122271120.171.934.2
ENTREZGMus musculusMm43059574441603129.967.334.9
ENTREZGMus musculusMm430A19412691190638.382.618.7
ENTREZGMus musculusMouse Genome 430A 2.019412691190638.382.618.7
ENTREZGMus musculusMm430B7115269544737.466.661.7
ENTREZGMus musculusMm74Av12331214679039.277.231.9
ENTREZGMus musculusMm74Av21775229750837.575.426.1
ENTREZGMus musculusMm74Bv22738206543939.574.340.3
ENTREZGMus musculusMm74Cv24252161256031.55869.4
ENTREZGRattus norvegicusRn23033695731092528.966.933.4
ENTREZGRattus norvegicusRn230A2315430818938.180.928.2
ENTREZGRattus norvegicusRn230B323830836153369.754.2
ENTREZGRattus norvegicusRn34A1155156406822.477.629.4
REFSEQArabidopsis thalianaAtGenome13732977596375.396.942.5
REFSEQArabidopsis thalianaAtH1386374331782190.698.838.9
REFSEQBos taurusBovine3006392273675076.751.3
REFSEQCanis familiarisCfCanine21648325651956.872.897.1
REFSEQDrosophila melanogasterDmDrosophila2334689911030295.698.654.6
REFSEQDrosophila melanogasterDmGenome131078481910193.498.756.1
REFSEQDanio rerioDrZebrafish33696381520642.883.367.1
REFSEQGallus gallusGgChicken870334836065274.272.4
REFSEQHomo sapiensHs133A47979048848355.984.863.1
REFSEQHomo sapiensHs133Av247979048848355.984.863.1
REFSEQHomo sapiensHs133B60824319441044.868.172.6
REFSEQHomo sapiensHs133P7893124141259037.463.965.4
REFSEQHomo sapiensHs133X8161123071244841.365.466
REFSEQHomo sapiensHs95Av23412659556655886.165
REFSEQHomo sapiensHsFocus29916027550367.793.362.6
REFSEQMus musculusMm11KsubA19582448322752.685.960
REFSEQMus musculusMm11KsubB13941615215040.876.461.9
REFSEQMus musculusMm430879098511171044.869.764
REFSEQMus musculusMm430A42626228930659.284.754.2
REFSEQMus musculusMouse Genome 430A 2.042626228930659.284.754.2
REFSEQMus musculusMm430B80554647327046.368.481.2
REFSEQMus musculusMm74Av135553694533254.579.459.9
REFSEQMus musculusMm74Av231644086589551.677.557.6
REFSEQMus musculusMm74Bv240523467376647.175.468.9
REFSEQMus musculusMm74Cv247432090164832.858.783.7
REFSEQOryza sativaOsRice406220821933NA4.399
REFSEQRattus norvegicusRn230742511816685447.27075.7
REFSEQRattus norvegicusRn230A48037480568759.582.669.4
REFSEQRattus norvegicusRn230B53766073147644.272.889.6
REFSEQRattus norvegicusRn34A18202359338553.581.857.7
UGBos taurusBovine50696831123752.386.535.7
UGCanis familiarisCfCanine268724299867034.270.158.1
UGDanio rerioDrZebrafish48781341758134.28347.9
UGGallus gallusGgChicken6677640010472357458.2
UGHomo sapiensHs133A22129541089142.681.226.2
UGHomo sapiensHs133Av221929951085042.681.326.4
UGHomo sapiensHs133B63031929891451.682.650.4
UGHomo sapiensHs133P1015327511943141.778.143.4
UGHomo sapiensHs133X103892718190864577.744.3
UGHomo sapiensHs95Av212641560659945.180.134.7
UGHomo sapiensHsFocus1138554693052.889.921.6
UGMus musculusMm11KsubA5182735163141.180.669.3
UGMus musculusMm11KsubB560796197229.775.246.4
UGMus musculusMm430586317091773547.18133.3
UGMus musculusMm430A18197941157649.983.821.6
UGMus musculusMouse Genome 430A 2.018197941157649.983.821.6
UGMus musculusMm430B50391306802154.384.446.1
UGMus musculusMm74Av122331352596648.579.641.9
UGMus musculusMm74Av216061194659247.881.634.2
UGMus musculusMm74Bv22477777622446.28238
UGMus musculusMm74Cv22989651385141.775.953.1
UGRattus norvegicusRn230599313031733857.588.231.3
UGRattus norvegicusRn230A286875910114618927.9
UGRattus norvegicusRn230B3760666840258.690.235.9
UGRattus norvegicusRn34A1050676400043.979.134.8
1. Identical probe sets are those with identical probe contents in Affymetrix annotation and the custome annotation.
2. Since most probe level data analysis algorithms have built mechanism for dealing with outliers, probe sets that differ only a couple of probes from the Affymetrix probe sets should have similar probe set level signal values.
3. These are probe sets that are supposed to represent the same target but there are >=50% probe content difference between the Affymetrix and custom probe set definition.

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