Home > Service > Custom CDF > Description > Statistics

Statistics of Affymetrix and Custom CDF Files (Version 9)

Table 1: Probe utilization
SpeciesChipProbe countUG (%)REFSEQ (%)ENTREZG (%)ENSG (%)ENST (%)ENSE (%)VEGAG (%)VEGAT (%)VEGAE (%)TAIR (%)
Arabidopsis thalianaAtGenome130858NA89.3NANANANANANANA89.4
Arabidopsis thalianaAtH1250103NA90.5NANANANANANANA90.9
Bos taurusBovine26412644.252.54419.226.615.6NANANANA
Canis familiarisCfCanine247165029.42.250.946.653.238.9NA.1NANA
Drosophila melanogasterDmDrosophila22627667676.3NA73.976.472.3NANANANA
Drosophila melanogasterDmGenome119518693.293.1NA93.293.290.6NANANANA
Danio rerioDrZebrafish24801342.347.924.525.128.123.2NA15.7NANA
Gallus gallusGgChicken42282548.413.843.237.943.332.1NANANANA
Homo sapiensHs133A24679969.672.167.76871.363.36271.258.3NA
Homo sapiensHs133Av224679969.672.167.76871.363.36271.258.3NA
Homo sapiensHs133B24833651.633.730.83334.131.335.440.533.9NA
Homo sapiensHs133P60315857.947.944.74648.143.246.352.844NA
Homo sapiensHs133X67280455.94643.344.64643.845.651.244.8NA
Homo sapiensHs95Av219769571.674.770.570.573.668.563.773.162.1NA
Homo sapiensHsEx10stv2538365429.621.821.721.921.521.622.424.322.1NA
Homo sapiensHsFocus9734977.784.879.978.582.272.268.680.163.6NA
Homo sapiensHsNuGOHs1a52018026440769.569.565.869.972.865.960.669.657.5NA
Macaca mulattaRhesus6671868NA48.536.337.134.4NANANANA
Mus musculusMm11KsubA13018062.56459.556.158.55518.619.318.3NA
Mus musculusMm11KsubB11848048.551.945.644.749.843.114.215.613.7NA
Mus musculusMm43049537460.351.847.345.948.542.816.817.616NA
Mus musculusMm430A24886471.873.267.265.169.260.321.622.820.4NA
Mus musculusMouse Genome 430A 2.024886471.873.267.265.1NA60.321.622.820.4NA
Mus musculusMm430B24761048.630.227.326.527.725.11212.411.6NA
Mus musculusMm74Av120064155.356.251.449.252.347.516.317.115.9NA
Mus musculusMm74Av219667061.96458.65659.654.218.619.618.2NA
Mus musculusMm74Bv21958085951.146.444.746.643.617.317.817NA
Mus musculusMm74Cv218147432.820.118.817.718.217.47.887.8NA
Mus musculusMmEx10stv1473763429.522.321.421.221.220.98.28.28.1NA
Mus musculusMmNuGOMm1a52017726163565.163.558.858.561.954.219.12018NA
Oryza sativaOsRice629427NA45.8NANANANANANANANA
Pan troglodytesHs133A246799NA71.65046.249.841.6NANANANA
Pan troglodytesHs133Av2246799NA71.65046.249.841.6NANANANA
Pan troglodytesHs133B248336NA31.227.820.321.718.6NANANANA
Pan troglodytesHs133P603158NA46.335.330.232.527.4NANANANA
Pan troglodytesHs133X672804NA44.33428.530.327.6NANANANA
Pan troglodytesHs95Av2197695NA74.152.948.151.446.1NANANANA
Pan troglodytesHsEx10stv25383654NA20.318.716.216.415.4NANANANA
Pan troglodytesHsFocus97349NA85.356.253.157.247.1NANANANA
Pan troglodytesHsNuGOHs1a520180264407NA66.548.944.64840.6NANANANA
Rattus norvegicusRn2303414596146.440.431.833.828.6NANANANA
Rattus norvegicusRn230A17452668.161.453.74446.739.4NANANANA
Rattus norvegicusRn230B16803353.530.926.619.220.317.5NANANANA
Rattus norvegicusRn34A13913763.964.954.84952.846.3NANANANA
Rattus norvegicusRnEx10stv1402777623.922.921.521.621.621.3NANANANA

Table 2. Target Count for Affymetrix and Custom Probe Sets
SpeciesChipAffy-UG1Affy-ENSG2Affy-REFSEQ3UGREFSEQENTREZGENSGENSTENSEVEGAGVEGATVEGAETAIR
Arabidopsis thalianaAtGenome1280NA7336NA8644NANANANANANANA7218
Arabidopsis thalianaAtH1NANA21684NA24462NANANANANANANA21074
Bos taurusBovine158435260103739454121899460537691397636NANANANA
Canis familiarisCfCanine21544916612170021096574415809165102192731939NA58NANA
Drosophila melanogasterDmDrosophila2NA13636136481301819250NA135291909920479NANANANA
Drosophila melanogasterDmGenome1NA12169122081181717559NA122151737720475NANANANA
Danio rerioDrZebrafish1251754588575706691464505477662037491NA3052NANA
Gallus gallusGgChicken16366121721230916388388812516119781651923693NANANANA
Homo sapiensHs133A125571198413280116391748912058118302384722400119623967427292NA
Homo sapiensHs133Av2125151198413280116391748912058118302384722400119623967427292NA
Homo sapiensHs133B129786431104929716865161276287113931074672201934114056NA
Homo sapiensHs133P240031732220483200772504017637172093412034700186455841944439NA
Homo sapiensHs133X239191735320609197292476717497170293308631756184965577240529NA
Homo sapiensHs95Av277058297907780381219782068069160791491181402649118081NA
Homo sapiensHsEx10stv2NANANA43943354942397626220416242334602987292868296228NA
Homo sapiensHsFocus79517764849474451144478947690148141207076552468214136NA
Homo sapiensHsNuGOHs1a520180NANANA162412257316358171992996426094163604568528955NA
Macaca mulattaRhesusNANANA3640NA16175139302394229324NANANANA
Mus musculusMm11KsubA214341375186426859164219399251636048129227032646NA
Mus musculusMm11KsubB25063063354426963964278927633713548883923152628NA
Mus musculusMm43020590157262050017867247111629715758210432543849301172411881NA
Mus musculusMm430A129251188513568119291667212152117141572418765350685968431NA
Mus musculusMouse Genome 430A 2.012925118851356811929166721215211714NA18765350685968431NA
Mus musculusMm430B118425494113258627103855400540068787688215541174021NA
Mus musculusMm74Av18061696488877073959669376653868910225208645994569NA
Mus musculusMm74Av280607712905975631061276637351960311309231151105086NA
Mus musculusMm74Bv2832255627818664992085419529768367900188039433903NA
Mus musculusMm74Cv2653735196391421341732575245330853102102218621674NA
Mus musculusMmEx10stv1NANANA341074087322659227613006719857587212468597583NA
Mus musculusMmNuGOMm1a520177NANANA158042318115105152971886920085476991108383NA
Oryza sativaOsRice21718NA2339NA24015NANANANANANANANA
Pan troglodytesHs133ANANANANA1706510766102631653416218NANANANA
Pan troglodytesHs133Av2NANANANA1706510766102631653416218NANANANA
Pan troglodytesHs133BNANANANA74326425503275057271NANANANA
Pan troglodytesHs133PNANANANA2312116098149012379924832NANANANA
Pan troglodytesHs133XNANANANA2288215754144112270123117NANANANA
Pan troglodytesHs95Av2NANANANA11981742068901086711026NANANANA
Pan troglodytesHsEx10stv2NANANANA24833249062049631515173932NANANANA
Pan troglodytesHsFocusNANANANA115366807650598248491NANANANA
Pan troglodytesHsNuGOHs1a520180NANANANA2072314898140942019818064NANANANA
Rattus norvegicusRn23020581940514279168871880611562100361344014346NANANANA
Rattus norvegicusRn230A124067102104901041313277867875451006810255NANANANA
Rattus norvegicusRn230B1105331436852803175983944322642294470NANANANA
Rattus norvegicusRn34A499139945205455458014260394057197474NANANANA
Rattus norvegicusRnEx10stv1NANANA2859636744213342192031616192301NANANANA

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 taurusBovine13501466391020.47944.4
ENSGCanis familiarisCfCanine210819791553118.278.515.5
ENSGDrosophila melanogasterDmDrosophila22861791335066.6993.5
ENSGDrosophila melanogasterDmGenome11742201199592.5993.3
ENSGDanio rerioDrZebrafish1283601417516.478.834.5
ENSGGallus gallusGgChicken11819871099120.777.819.9
ENSGHomo sapiensHs133A6555011132942.191.111.1
ENSGHomo sapiensHs133Av26555011132942.191.111.1
ENSGHomo sapiensHs133B508364592350.691.214.1
ENSGHomo sapiensHs133P930817163923990.411.3
ENSGHomo sapiensHs133X10687441628549.690.611.7
ENSGHomo sapiensHs95Av2516288778148.39111.3
ENSGHomo sapiensHsFocus423349734150.393.510.6
ENSGMus musculusMm11KsubA315170382239.687.914.5
ENSGMus musculusMm11KsubB434134262919.77524.7
ENSGMus musculusMm4308538851487340.789.412.2
ENSGMus musculusMm430A7035321118241.490.711.6
ENSGMus musculusMouse Genome 430A 2.07035321118241.490.711.6
ENSGMus musculusMm430B546452494851.69018.3
ENSGMus musculusMm74Av165934863054388.116.5
ENSGMus musculusMm74Av2728367698438.280.817.3
ENSGMus musculusMm74Bv2526261503644.986.516.6
ENSGMus musculusMm74Cv21240174227937.370.344.7
ENSGRattus norvegicusRn2307521383865335.586.422.1
ENSGRattus norvegicusRn230A506949659640.490.319.7
ENSGRattus norvegicusRn230B473556267034.383.330.5
ENSGRattus norvegicusRn34A345291364922.78318.2
ENTREZGBos taurusBovine27251177828330.373.137.1
ENTREZGCanis familiarisCfCanine214192211558817.774.414.2
ENTREZGDanio rerioDrZebrafish6390750375515.772.769
ENTREZGGallus gallusGgChicken160418051071119.466.530.3
ENTREZGHomo sapiensHs133A16923261173237.782.218.1
ENTREZGHomo sapiensHs133Av216923261173237.782.218.1
ENTREZGHomo sapiensHs133B480024758803565.451.6
ENTREZGHomo sapiensHs133P37684981713925.260.629.9
ENTREZGHomo sapiensHs133X40645331696432.562.330.9
ENTREZGHomo sapiensHs95Av21166233797344.783.718.5
ENTREZGHomo sapiensHsFocus815201769349.592.112.9
ENTREZGMus musculusMm11KsubA1301146407338.184.130.5
ENTREZGMus musculusMm11KsubB87797269219.771.834.3
ENTREZGMus musculusMm43060573661593129.465.835.7
ENTREZGMus musculusMm430A19702751187737.681.119.4
ENTREZGMus musculusMouse Genome 430A 2.019702751187737.681.119.4
ENTREZGMus musculusMm430B7329167523336.866.163
ENTREZGMus musculusMm74Av12408224671338.176.333.1
ENTREZGMus musculusMm74Av21862242742136.474.527.4
ENTREZGMus musculusMm74Bv22909151526838.873.442
ENTREZGMus musculusMm74Cv24348111246430.957.870.2
ENTREZGRattus norvegicusRn23033596271093529.166.833.6
ENTREZGRattus norvegicusRn230A2308482819638.280.928.5
ENTREZGRattus norvegicusRn230B3235326361833.169.654.3
ENTREZGRattus norvegicusRn34A1149186407422.477.329.8
REFSEQArabidopsis thalianaAtGenome13452653599175.596.940.3
REFSEQArabidopsis thalianaAtH1376865461791691.39936.7
REFSEQBos taurusBovine19343750843951.877.743.1
REFSEQCanis familiarisCfCanine21648122352156.872.797.1
REFSEQDrosophila melanogasterDmDrosophila2337089721027895.798.654.7
REFSEQDrosophila melanogasterDmGenome131198470908993.498.756.2
REFSEQDanio rerioDrZebrafish37694340480638.477.566.6
REFSEQGallus gallusGgChicken8697276361252.174.372.2
REFSEQHomo sapiensHs133A47788987850256.584.862.9
REFSEQHomo sapiensHs133Av247788987850256.584.862.9
REFSEQHomo sapiensHs133B60884247440444.568.172.4
REFSEQHomo sapiensHs133P7803123601268037.763.965.1
REFSEQHomo sapiensHs133X8071122291253841.665.365.6
REFSEQHomo sapiensHs95Av234266546565157.986.165
REFSEQHomo sapiensHsFocus29905940550468.593.462.4
REFSEQMus musculusMm11KsubA19382669324752.385.860.8
REFSEQMus musculusMm11KsubB13681788217640.476.262.8
REFSEQMus musculusMm4308653128641184744.169.666.9
REFSEQMus musculusMm430A41947298937458.384.656.3
REFSEQMus musculusMouse Genome 430A 2.041947298937458.384.656.3
REFSEQMus musculusMm430B80027062332345.568.183.5
REFSEQMus musculusMm74Av135114220537653.579.261.2
REFSEQMus musculusMm74Av231124665594750.577.359
REFSEQMus musculusMm74Bv24021541137974675.473.3
REFSEQMus musculusMm74Cv247292511166232.458.884.3
REFSEQOryza sativaOsRice406220821933NA4.399
REFSEQRattus norvegicusRn23073471187469324870.875.4
REFSEQRattus norvegicusRn230A47347521575660.583.769
REFSEQRattus norvegicusRn230B53636109148944.57389.5
REFSEQRattus norvegicusRn34A17762372342955.683.457
UGBos taurusBovine76851296815850.186.253.7
UGCanis familiarisCfCanine260301546941937.781.545.7
UGDanio rerioDrZebrafish611966863983478.155.3
UGGallus gallusGgChicken64386460992832.476.958.6
UGHomo sapiensHs133A17177991084043.380.922.7
UGHomo sapiensHs133Av217108341080543.48123
UGHomo sapiensHs133B50031741797542.172.850.3
UGHomo sapiensHs133P625023241775335.471.138.7
UGHomo sapiensHs133X643322431748638.670.839.5
UGHomo sapiensHs95Av211071440659846.18032.5
UGHomo sapiensHsFocus1005499694654.890.619.7
UGMus musculusMm11KsubA5212646162242.880.168.9
UGMus musculusMm11KsubB569759193731.574.846.2
UGMus musculusMm430432015971627042.675.932
UGMus musculusMm430A17817851114451.683.722
UGMus musculusMouse Genome 430A 2.017817851114451.683.722
UGMus musculusMm430B4429121474134677.347
UGMus musculusMm74Av122421254581950.480.341.8
UGMus musculusMm74Av216381141642249.382.134.4
UGMus musculusMm74Bv22449776587344.779.939.3
UGMus musculusMm74Cv22987663355038.971.855.9
UGRattus norvegicusRn230495812641562351.181.531.4
UGRattus norvegicusRn230A2660667974659.486.727.4
UGRattus norvegicusRn230B3741719731250.78340.4
UGRattus norvegicusRn34A1047610394443.57834.5
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.

Comments and suggestions are welcome. You can pose your opinions and discuss relevant issues in our forum.

 

Comments, suggestions and problems? Discuss at our forum

 

Problem with this website? Email us at daimh@umich.edu  

 

İMicroArray Lab