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Statistics of Affymetrix and Custom CDF Files (Version 7)

Table 1: Probe utilization

Species Chip Probe count UG (%) REFSEQ (%) ENTREZG (%) ENSG4 (%) ENST4 (%) ENSE4 (%) TIGR (%)
Arabidopsis thaliana AtGenome 130858 NA 92 NA NA NA NA 96.9
Arabidopsis thaliana AtH1 250103 NA 94.8 NA NA NA NA 98.2
Canis familiaris CfCanine2 471650 32.6 1.9 50.9 50.2 59.1 42.2 NA
Drosophila melanogaster DmDrosophila2 262766 74.1 76.4 NA 73.5 76.1 72 NA
Drosophila melanogaster DmGenome1 195186 92.1 93.2 NA 93.1 93.2 90.5 NA
Danio rerio DrZebrafish 248013 21.1 39.5 21.1 22.4 26.1 20.7 NA
Gallus gallus GgChicken 422825 39.8 12.5 NA 36.6 40.8 30.7 NA
Homo sapiens Hs133A 246799 70.9 71.4 67.4 70.2 73.8 65.7 NA
Homo sapiens Hs133Av2 246799 70.9 71.4 67.4 70.2 73.8 65.7 NA
Homo sapiens Hs133B 248336 49 32.1 31 36.3 38.1 34.5 NA
Homo sapiens Hs133P 603158 56.8 47.3 45 49.5 52 46.7 NA
Homo sapiens Hs133X 672804 54.5 45.3 43.7 48.3 50.1 47.5 NA
Homo sapiens Hs95Av2 197695 73.5 73.5 70.1 72.2 75.6 70.3 NA
Homo sapiens HsEx10stv2 5383654 28.6 21 21.6 25 24.9 24.7 NA
Homo sapiens HsFocus 97349 80.1 84.4 79.5 79.5 83.4 73.3 NA
Mus musculus Mm11KsubA 130180 61.8 62.4 58.3 57.2 59.5 56.1 NA
Mus musculus Mm11KsubB 118480 48.6 51.4 45.2 44.5 49.5 42.9 NA
Mus musculus Mm430 495374 58.9 50.3 46.6 47.4 50 44.3 NA
Mus musculus Mm430A 248864 71 71.3 65.8 66.6 70.6 61.9 NA
Mus musculus Mm430B 247610 46.6 29.2 27.3 28 29.2 26.7 NA
Mus musculus Mm74Av1 200641 54.9 54.6 50.7 50.2 53.3 48.6 NA
Mus musculus Mm74Av2 196670 61.1 62 57.5 57 60.5 55.2 NA
Mus musculus MmEx10stv1 4737634 28.8 22 22.3 21.7 21.7 21.5 NA
Oryza sativa OsRice 629427 NA 37.4 NA NA NA NA 74.2
Pan troglodytes Hs133A NA NA NA NA 50.2 NA 45.9 NA
Pan troglodytes Hs133Av2 NA NA NA NA 50.2 NA 45.9 NA
Pan troglodytes Hs133B NA NA NA NA 21.3 NA 19.8 NA
Pan troglodytes Hs133P NA NA NA NA 32.6 NA 30 NA
Pan troglodytes Hs133X NA NA NA NA 31.2 NA 30.4 NA
Pan troglodytes Hs95Av2 NA NA NA NA 52.4 NA 50.5 NA
Pan troglodytes HsEx10stv2 NA NA NA NA 16.5 NA 15.9 NA
Pan troglodytes HsFocus NA NA NA NA 57.7 NA 52.2 NA
Rattus norvegicus Rn230 341459 59.8 38.3 32.8 25.9 27.9 22.8 NA
Rattus norvegicus Rn230A 174526 67.1 53.3 45.5 37.4 40.1 32.9 NA
Rattus norvegicus Rn230B 168033 52.2 22.8 19.8 13.9 15.1 12.3 NA
Rattus norvegicus Rn34A 139137 64.9 61.7 51.3 46.8 50.6 44.2 NA
Rattus norvegicus RnEx10stv1 4027776 25.1 21.7 21.4 20.4 20.4 20.1 NA
Vitis vinifera VvGrape 261838 NA NA NA NA NA NA 68.9

Table 2. Target Count for Affymetrix and Custom Probe Sets

Species Chip Affy-UG1 Affy-ENSG2 Affy-REFSEQ3 UG REFSEQ ENTREZG ENSG4 ENST4 ENSE4 TIGR
Arabidopsis thaliana AtGenome 1273 NA 7337 NA 9018 NA NA NA NA 10805
Arabidopsis thaliana AtH1 NA NA 21695 NA 26270 NA NA NA NA 30454
Canis familiaris CfCanine2 16989 18136 16968 12228 643 15861 17287 29346 37422 NA
Drosophila melanogaster DmDrosophila2 NA 13626 13627 13009 19185 NA 13420 18882 20201 NA
Drosophila melanogaster DmGenome1 NA 12205 12248 11889 17446 NA 12178 17217 20346 NA
Danio rerio DrZebrafish 12909 4927 7998 3947 8920 4320 4290 6284 6661 NA
Gallus gallus GgChicken 18356 12698 13775 14131 3618 NA 12631 16377 23028 NA
Homo sapiens Hs133A 12790 11868 12986 11695 17881 12133 18672 36175 35192 NA
Homo sapiens Hs133Av2 12758 11868 12986 11695 17881 12133 18672 36175 35192 NA
Homo sapiens Hs133B 13312 5848 10114 8893 9274 6306 9819 17372 16935 NA
Homo sapiens Hs133P 24172 17083 19412 19278 26714 17752 27686 53171 55522 NA
Homo sapiens Hs133X 24100 17090 19497 19100 26272 17622 27319 51033 50640 NA
Homo sapiens Hs95Av2 7837 8146 8977 8096 12481 8292 12610 23747 23140 NA
Homo sapiens HsEx10stv2 NA NA NA 35967 35905 22672 48749 83497 387466 NA
Homo sapiens HsFocus 8182 7604 8507 7607 11319 7947 11929 21833 18354 NA
Mus musculus Mm11KsubA 2165 4175 5060 4230 5689 4241 4638 6534 7365 NA
Mus musculus Mm11KsubB 2573 3090 3470 2721 4054 2879 3163 5001 6736 NA
Mus musculus Mm430 20810 15829 17915 18127 24787 16300 18288 27461 31331 NA
Mus musculus Mm430A 13017 11928 13208 11949 16354 12141 13526 20622 23201 NA
Mus musculus Mm430B 12116 5522 9010 8808 10600 5577 6351 8679 9329 NA
Mus musculus Mm74Av1 8218 7086 8723 7088 9354 7010 7746 11210 12696 NA
Mus musculus Mm74Av2 8216 7845 8868 7518 10296 7704 8546 12364 14029 NA
Mus musculus MmEx10stv1 NA NA NA 36049 43259 26256 27429 45244 244493 NA
Oryza sativa OsRice 28342 NA NA NA 24027 NA NA NA NA 45047
Pan troglodytes Hs133A NA NA NA NA NA NA 10663 NA 16583 NA
Pan troglodytes Hs133Av2 NA NA NA NA NA NA 10663 NA 16583 NA
Pan troglodytes Hs133B NA NA NA NA NA NA 5098 NA 7296 NA
Pan troglodytes Hs133P NA NA NA NA NA NA 15497 NA 25364 NA
Pan troglodytes Hs133X NA NA NA NA NA NA 15088 NA 23593 NA
Pan troglodytes Hs95Av2 NA NA NA NA NA NA 7220 NA 11170 NA
Pan troglodytes HsEx10stv2 NA NA NA NA NA NA 22352 NA 175067 NA
Pan troglodytes HsFocus NA NA NA NA NA NA 6716 NA 8675 NA
Rattus norvegicus Rn230 21227 8400 13534 16995 11970 10265 8704 11539 12447 NA
Rattus norvegicus Rn230A 12475 6299 10040 10362 9083 7733 6621 8705 8993 NA
Rattus norvegicus Rn230B 11531 2666 6241 8063 3733 3248 2538 3384 3635 NA
Rattus norvegicus Rn34A 5062 3852 5032 4647 4794 4040 3748 5304 7106 NA
Rattus norvegicus RnEx10stv1 NA NA NA 35567 22417 20342 21010 30620 183113 NA
Vitis vinifera VvGrape 10821 NA NA NA NA NA NA NA NA 11348

Table 3. Affy vs Custom

Cdf Species Chip Affy Only Custom Only Shared Percentage of
identical probesets
in shared targets		 Percentage of
probesets with
difference<=25%
in shared targets		 Percentage of
probesets with
difference>50%
in all targets
ENSG4 Canis familiaris CfCanine2 942 93 17194 24.2 85.1 7.6
ENSG4 Drosophila melanogaster DmDrosophila2 229 23 13397 67.1 99.1 1.9
ENSG4 Drosophila melanogaster DmGenome1 124 97 12081 92.6 99.1 2
ENSG4 Danio rerio DrZebrafish 1191 554 3736 16.7 80.4 34.6
ENSG4 Gallus gallus GgChicken 1671 1604 11027 19.9 71.7 28.9
ENSG4 Homo sapiens Hs133A 660 7464 11208 41.6 90.6 43.2
ENSG4 Homo sapiens Hs133Av2 660 7464 11208 41.6 90.6 43.2
ENSG4 Homo sapiens Hs133B 556 4527 5292 48.9 90.2 49.9
ENSG4 Homo sapiens Hs133P 952 11555 16131 39.1 89.6 44.8
ENSG4 Homo sapiens Hs133X 1115 11344 15975 49.9 89.8 44.9
ENSG4 Homo sapiens Hs95Av2 499 4963 7647 46.6 90.4 43
ENSG4 Homo sapiens HsFocus 407 4732 7197 49.8 93.3 42.3
ENSG4 Mus musculus Mm11KsubA 355 818 3820 39.4 88.6 26.3
ENSG4 Mus musculus Mm11KsubB 499 572 2591 19.5 75.7 34.9
ENSG4 Mus musculus Mm430 942 3401 14887 39.8 87.8 24.3
ENSG4 Mus musculus Mm430A 764 2362 11164 40.5 89.5 23.5
ENSG4 Mus musculus Mm430B 649 1478 4873 50.2 88.3 31.9
ENSG4 Mus musculus Mm74Av1 738 1398 6348 42.5 87.9 27.7
ENSG4 Mus musculus Mm74Av2 827 1528 7018 37.9 80.7 28.4
ENSG4 Rattus norvegicus Rn230 921 1225 7479 30 84 25.2
ENSG4 Rattus norvegicus Rn230A 569 891 5730 34.9 89.1 22.2
ENSG4 Rattus norvegicus Rn230B 569 441 2097 25 77.8 36.3
ENSG4 Rattus norvegicus Rn34A 357 253 3495 22.2 83 18.5
ENTREZG Canis familiaris CfCanine2 1408 264 15597 18.2 77.4 13.8
ENTREZG Danio rerio DrZebrafish 6824 1116 3204 14.8 71.8 74.3
ENTREZG Homo sapiens Hs133A 1520 389 11744 36 80.8 17.5
ENTREZG Homo sapiens Hs133Av2 1520 389 11744 36 80.8 17.5
ENTREZG Homo sapiens Hs133B 4719 477 5829 33.2 63.8 53.2
ENTREZG Homo sapiens Hs133P 3431 712 17040 23.6 58.9 29.9
ENTREZG Homo sapiens Hs133X 3646 726 16896 30.7 60.6 30.5
ENTREZG Homo sapiens Hs95Av2 1108 288 8004 43.3 82.7 18.8
ENTREZG Homo sapiens HsFocus 818 224 7723 48.3 91.8 13.2
ENTREZG Mus musculus Mm11KsubA 1294 218 4023 37 83.4 31.8
ENTREZG Mus musculus Mm11KsubB 828 189 2690 19.3 70.7 35.4
ENTREZG Mus musculus Mm430 5925 598 15702 27.3 63.4 36.9
ENTREZG Mus musculus Mm430A 1895 373 11768 35.2 78.8 20.2
ENTREZG Mus musculus Mm430B 7244 502 5075 34.6 64.6 64.8
ENTREZG Mus musculus Mm74Av1 2424 350 6660 36.3 74.3 34.8
ENTREZG Mus musculus Mm74Av2 1863 351 7353 34.8 73 28.8
ENTREZG Rattus norvegicus Rn230 3743 361 9904 25 62.2 38.1
ENTREZG Rattus norvegicus Rn230A 2734 329 7404 33.3 76 33.7
ENTREZG Rattus norvegicus Rn230B 3138 100 3148 24.1 61.1 57
ENTREZG Rattus norvegicus Rn34A 1252 192 3848 20.8 73.5 33.4
REFSEQ Arabidopsis thaliana AtGenome 1047 2728 6290 79.7 96.7 37.8
REFSEQ Arabidopsis thaliana AtH1 2966 7541 18729 93.5 99.3 36
REFSEQ Canis familiaris CfCanine2 16349 24 619 54.4 70.9 96.5
REFSEQ Drosophila melanogaster DmDrosophila2 3209 8767 10418 96.5 98.9 53.5
REFSEQ Drosophila melanogaster DmGenome1 2983 8181 9265 93.4 98.6 54.8
REFSEQ Danio rerio DrZebrafish 2369 3291 5629 38 78.8 54.9
REFSEQ Gallus gallus GgChicken 10337 180 3438 54.3 75.2 76.3
REFSEQ Homo sapiens Hs133A 3997 8892 8989 57.2 83.7 60.2
REFSEQ Homo sapiens Hs133Av2 3997 8892 8989 57.2 83.7 60.2
REFSEQ Homo sapiens Hs133B 5463 4623 4651 43.4 67.1 71.1
REFSEQ Homo sapiens Hs133P 5853 13155 13559 37.7 62.1 62.6
REFSEQ Homo sapiens Hs133X 6071 12846 13426 41.3 63.8 62.8
REFSEQ Homo sapiens Hs95Av2 3015 6519 5962 56.5 85 63
REFSEQ Homo sapiens HsFocus 2756 5568 5751 70.4 93.4 59.6
REFSEQ Mus musculus Mm11KsubA 1191 1821 3868 52.8 84.7 46.9
REFSEQ Mus musculus Mm11KsubB 828 1412 2642 41 75.4 51
REFSEQ Mus musculus Mm430 3113 9985 14802 41.9 67.3 51.2
REFSEQ Mus musculus Mm430A 1911 5057 11297 55.1 82.2 40.3
REFSEQ Mus musculus Mm430B 4523 6113 4487 45 67.4 72.9
REFSEQ Mus musculus Mm74Av1 2294 2925 6429 50.4 76.7 48.1
REFSEQ Mus musculus Mm74Av2 1776 3204 7092 47.9 75.5 44.9
REFSEQ Rattus norvegicus Rn230 2947 1383 10587 42.2 66.9 35.5
REFSEQ Rattus norvegicus Rn230A 2085 1128 7955 55.3 80.3 31.9
REFSEQ Rattus norvegicus Rn230B 2909 401 3332 37.3 65.8 54.9
REFSEQ Rattus norvegicus Rn34A 875 637 4157 51.5 80.4 31.2
UG Canis familiaris CfCanine2 6013 1252 10976 37.7 82.1 41.1
UG Danio rerio DrZebrafish 9709 747 3200 20.1 81.7 78.2
UG Gallus gallus GgChicken 8808 4583 9548 37.3 78.3 60.5
UG Homo sapiens Hs133A 1601 506 11189 47.5 82.6 19.5
UG Homo sapiens Hs133Av2 1589 526 11169 47.6 82.7 19.6
UG Homo sapiens Hs133B 5189 770 8123 43.1 72.1 47.1
UG Homo sapiens Hs133P 5939 1045 18233 35.8 70.4 34.3
UG Homo sapiens Hs133X 6075 1075 18025 40.2 69.1 35.6
UG Homo sapiens Hs95Av2 961 1220 6876 52.8 82.3 28
UG Homo sapiens HsFocus 898 323 7284 60.9 92.1 15.8
UG Mus musculus Mm11KsubA 558 2623 1607 45.1 80.3 69.2
UG Mus musculus Mm11KsubB 592 740 1981 29.9 72 47.1
UG Mus musculus Mm430 4279 1596 16531 41.5 74.2 32.1
UG Mus musculus Mm430A 1842 774 11175 51.2 83.5 22.5
UG Mus musculus Mm430B 4492 1184 7624 43.7 73.8 47.5
UG Mus musculus Mm74Av1 2345 1215 5873 44.2 71.3 43.7
UG Mus musculus Mm74Av2 1735 1037 6481 44.6 74.1 35.8
UG Rattus norvegicus Rn230 5716 1484 15511 49.2 80.3 34.9
UG Rattus norvegicus Rn230A 2850 737 9625 57.7 85.7 29.4
UG Rattus norvegicus Rn230B 4343 875 7188 48.3 81.3 44.8
UG Rattus norvegicus Rn34A 1058 643 4004 42.5 78 35
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.
4. Include definition from CORE and VEGA. Some of the definition may be redundant.

 

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