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Statistics of Affymetrix and Custom CDF Files (Version 2)

Table 1. Target Count for Affymetrix and Custom Probe Sets

Species Chiptype Affy-UG1 Affy-ENSG2 Affy-Refseq3 UG DoTS Refseq EntrezG ENSG3 ENST3 ENSE3 Affy-SNP UG-SNP
Hs Hs133A 12755 11569 12037 12764 101619 15639 2825 11394 16885 18091 22169 12610
Hs Hs133Av2 N/A N/A N/A 12764 101619 15639 2825 11394 16885 18091 22169 12610
Hs Hs133B 12876 7129 7539 9051 56590 6838 1682 5285 7218 7603 22562 8999
Hs Hs133P 24410 15445 16389 21276 163556 22153 4616 16308 23961 27325 54540 21088
Hs Hs133X 13507 15442 16371 21065 153882 21941 4497 15999 22896 24694 60993 20893
Hs Hs95Av2 7835 8073 8374 8748 67911 10797 1919 7615 11029 11995 12537 8675
Hs HsFocus N/A N/A N/A 7996 55623 10359 1747 7438 10471 9793 8727 7903
Mm Mm430 24388 13313 14448 23411 95998 16623 15271 14820 11602 22860 N/A N/A
Mm Mm430A 12961 11160 11891 13280 66391 12527 11479 11090 8750 17069 N/A N/A
Mm Mm430B 14224 4936 5479 12373 32871 5002 4660 4761 3500 6506 N/A N/A
Mm Mm74Av2 7685 7515 8004 8635 39895 7721 7111 6898 5261 10196 N/A N/A
Pt Hs133A N/A N/A N/A 11366 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133Av2 N/A N/A N/A 11367 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133B N/A N/A N/A 8401 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133P N/A N/A N/A 19245 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133X N/A N/A N/A 19037 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs95Av2 N/A N/A N/A 7816 N/A N/A N/A N/A N/A N/A N/A N/A
Pt HsFocus N/A N/A N/A 7111 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230 20428 4039 4670 18172 N/A 9200 8644 7064 8759 9191 N/A N/A
Rn Rn230A 12030 3960 4503 10756 N/A 7058 6591 5280 6544 6620 N/A N/A
Rn Rn230B 10372 584 742 8554 N/A 2536 2396 2015 2475 2629 N/A N/A
Rn Rn34A 4857 2970 3312 5387 N/A 4082 3764 3263 4269 6193 N/A N/A

 

1. Affy-UG is the count of unique UniGene ID that each Affymetrix GeneChip can represent. It is derived by mapping the "Representative Public ID" provided by Affymetrix to the Latest UniGene Build at the time of building our custom CDF files.
2. Affy-ENSG and Affy-Refseq counts are based on the latest version of Affymetrix GeneChip annotation files from www.affymetrix.com
3. To be consistent with Affymetrix annotation, only target numbers derived from the CORE division of ENSEMBL are listed here. Please refer to Table 5 for the distribution of custom probe sets across different ENSEMBL divisions.

Table 2. Affymetrix UG Probe Sets vs. Custom UG Probe Sets

Species Chiptype UGID Shared Affy Only UGID Custom Only UGID Identical Probe Sets1 Difference <= 3 Probes2 Difference >= 50%3
Hs Hs133A 11313 1442 1451 4951 7750 2327
Hs Hs133Av2 N/A N/A 12764 N/A N/A N/A
Hs Hs133B 7818 5058 1233 3357 4960 2041
Hs Hs133P 18824 5586 2452 6485 10177 5751
Hs Hs133X 8159 5348 12906 2311 3174 4386
Hs Hs95Av2 6877 958 1871 3366 4706 1423
Hs HsFocus N/A N/A 7996 N/A N/A N/A
Mm Mm430 19988 4400 3423 7229 12026 5031
Mm Mm430A 11395 1566 1885 4756 7640 2500
Mm Mm430B 10374 3850 1999 4008 6739 2196
Mm Mm74Av2 6321 1364 2314 2677 4036 1525
Pt Hs133A N/A N/A 11366 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11367 N/A N/A N/A
Pt Hs133B N/A N/A 8401 N/A N/A N/A
Pt Hs133P N/A N/A 19245 N/A N/A N/A
Pt Hs133X N/A N/A 19037 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7816 N/A N/A N/A
Pt HsFocus N/A N/A 7111 N/A N/A N/A
Rn Rn230 16208 4220 1964 6143 10896 3351
Rn Rn230A 9618 2412 1138 4037 7062 1659
Rn Rn230B 7567 2805 987 2964 5295 1348
Rn Rn34A 4055 802 1332 1230 2140 1326
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.

Table 3. Affymetrix UG Probe Sets vs. Custom UG-SNP Probe Sets

Species Chiptype UGID Shared Affy Only UGID Custom Only UGID Identical Probe Sets1 Difference <= 3 Probes2 Difference >= 50%3
Hs Hs133A 11188 1567 1576 2889 7251 2323
Hs Hs133Av2 N/A N/A 12764 N/A N/A N/A
Hs Hs133B 7781 5095 1270 2332 4779 2051
Hs Hs133P 18667 5743 2609 4013 9531 5763
Hs Hs133X 8116 5391 12949 1663 3066 4346
Hs Hs95Av2 6833 1002 1915 2127 4238 1476
Hs HsFocus N/A N/A 7996 N/A N/A N/A
Pt Hs133A N/A N/A 11366 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11367 N/A N/A N/A
Pt Hs133B N/A N/A 8401 N/A N/A N/A
Pt Hs133P N/A N/A 19245 N/A N/A N/A
Pt Hs133X N/A N/A 19037 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7816 N/A N/A N/A
Pt HsFocus N/A N/A 7111 N/A N/A N/A
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.

Table 4. Affymetrix ENSG Probe Sets vs. Custom ENSG Probe Sets

Species Chiptype ENSG Shared Affy Only ENSG Custom Only ENSG Identical Probe Sets1 Difference <= 3 Probes2 Difference >= 50%3
Hs Hs133A 10566 1003 828 3600 7079 1694
Hs Hs133Av2 N/A N/A 11394 N/A N/A N/A
Hs Hs133B 4414 2715 871 1523 2559 1279
Hs Hs133P 14371 1074 1937 3532 6938 4567
Hs Hs133X 14187 1255 1812 4536 7083 4565
Hs Hs95Av2 7124 949 491 2878 4649 1139
Hs HsFocus N/A N/A 7438 N/A N/A N/A
Mm Mm430 10761 2552 4059 2506 5491 3035
Mm Mm430A 9075 2085 2015 2530 5636 1727
Mm Mm430B 2452 2484 2309 726 1303 725
Mm Mm74Av2 5675 1840 1223 1671 3041 1310
Rn Rn230 2985 1054 4079 471 1462 1155
Rn Rn230A 2911 1049 2369 510 1591 948
Rn Rn230B 102 482 1913 12 45 38
Rn Rn34A 2250 720 1013 267 796 811
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.

Table 5. Affymetrix Refseq Probe Sets vs. Custom Refseq Probe Sets

Species Chiptype Refseq Shared Affy Only Refseq Custom Only Refseq Identical Probe sets1 Differnece <= 3 Probes2 Differnece >= 50%3
Hs Hs133A 8984 3053 6655 3186 6364 1386
Hs Hs133Av2 N/A N/A 15639 N/A N/A N/A
Hs Hs133B 3898 3641 2940 1273 2281 1141
Hs Hs133P 12799 3590 9354 3270 6538 4141
Hs Hs133X 12711 3660 9230 4175 6559 4143
Hs Hs95Av2 5913 2461 4884 2236 3912 917
Hs HsFocus N/A N/A 10359 N/A N/A N/A
Mm Mm430 12418 2030 4205 2677 6223 3836
Mm Mm430A 10303 1588 2224 2615 6272 2188
Mm Mm430B 2752 2727 2250 757 1466 833
Mm Mm74Av2 6391 1613 1330 1579 3298 1608
Rn Rn230 4086 584 5114 837 2446 1158
Rn Rn230A 3941 562 3117 912 2631 846
Rn Rn230B 230 512 2306 42 126 65
Rn Rn34A 2918 394 1164 481 1349 654

Table 6. Distribution of ENSEMBL Probe Sets in ENSEMBL CORE, ESTGENE and VEGA Databases

 

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 11394 16885 18091
Hs Hs133A EST 5997 10339 9407
Hs Hs133A VEGA 3174 4842 5188
Hs Hs133Av2 CORE 11394 16885 18091
Hs Hs133Av2 EST 5997 10339 9407
Hs Hs133Av2 VEGA 3174 4842 5188
Hs Hs133B CORE 5285 7218 7603
Hs Hs133B EST 2956 4721 4492
Hs Hs133B VEGA 1601 2490 2606
Hs Hs133P CORE 16308 23961 27325
Hs Hs133P EST 9363 15787 15002
Hs Hs133P VEGA 4472 7034 8039
Hs Hs133X CORE 15999 22896 24694
Hs Hs133X EST 8195 13458 12625
Hs Hs133X VEGA 4422 6827 7327
Hs Hs95Av2 CORE 7615 11029 11995
Hs Hs95Av2 EST 3505 5863 6094
Hs Hs95Av2 VEGA 2201 3211 3489
Hs HsFocus CORE 7438 10471 9793
Hs HsFocus EST 3292 5435 4486
Hs HsFocus VEGA 2052 2954 2743
Mm Mm430 CORE 14820 11602 22860
Mm Mm430 EST 8722 15232 13478
Mm Mm430A CORE 11090 8750 17069
Mm Mm430A EST 6423 11317 9812
Mm Mm430B CORE 4761 3500 6506
Mm Mm430B EST 2541 4231 3783
Mm Mm74Av2 CORE 6898 5261 10196
Mm Mm74Av2 EST 3549 6048 5801
Rn Rn230 CORE 7064 8759 9191
Rn Rn230 EST 7574 12316 11585
Rn Rn230A CORE 5280 6544 6620
Rn Rn230A EST 5077 8761 7669
Rn Rn230B CORE 2015 2475 2629
Rn Rn230B EST 2775 3911 4065
Rn Rn34A CORE 3263 4269 6193
Rn Rn34A EST 2506 4446 5017

Table 7. Probe Utilization in Affymetrix and Custom CDF files

 

Species Chiptype Affy Total Affy-UG Affy-ENSG Affy-Refseq UG DoTS Refseq EntrezG ENSG4 ENST4 ENSE4 Affy-SNP UG-SNP
Hs Hs133A 246799 220314 214160 219510 179140 198428 162349 32764 157823(163386) 158139(163673) 146278(151897) 230603 170000
Hs Hs133Av2 246799 N/A N/A N/A 179140 198428 162349 32764 157823(163386) 158139(163673) 146278(151897) 230603 170004
Hs Hs133B 248336 214911 126789 132762 116568 208766 68638 15912 71553(77340) 71746(77493) 67184(72975) 236685 112149
Hs Hs133P 603158 532303 384769 398831 345629 495100 257886 55376 254105(267012) 254683(267511) 236739(249717) 570872 330495
Hs Hs133X 672804 258949 414526 430152 374076 546684 277443 62371 272868(287728) 273008(287771) 266867(281758) 634588 356377
Hs Hs95Av2 197695 160615 175177 179005 146919 163103 134208 27511 130609(135424) 130904(135710) 126668(131499) 185369 139389
Hs HsFocus 97349 N/A N/A N/A 78447 81660 76395 15442 74039(75561) 74130(75637) 67869(69405) 90518 73888
Mm Mm430 495374 421072 290291 306789 317351 343740 201813 199246 200168(210152) 125950(166805) 185567(195126) N/A N/A
Mm Mm430A 248864 222386 210000 219029 182343 187750 149651 148062 147230(150908) 93321(120884) 135725(139333) N/A N/A
Mm Mm430B 247610 199720 81398 88964 136255 156554 52666 51746 53428(59731) 33005(46361) 50250(56200) N/A N/A
Mm Mm74Av2 196670 143242 159110 166911 124586 128653 103023 102172 100276(103372) 63250(82762) 96713(99755) N/A N/A
Pt Hs133A 191015 N/A N/A N/A 136073 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133Av2 191015 N/A N/A N/A 136076 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133B 194181 N/A N/A N/A 90447 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133P 465845 N/A N/A N/A 264409 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133X 514390 N/A N/A N/A 284981 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs95Av2 155376 N/A N/A N/A 113050 N/A N/A N/A N/A N/A N/A N/A N/A
Pt HsFocus 75612 N/A N/A N/A 59265 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230 341459 288915 67478 75816 195421 N/A 88402 84620 58725(95913) 59924(97411) 48076(84976) N/A N/A
Rn Rn230A 174526 158763 59569 65542 111640 N/A 65580 63013 43554(65849) 44425(66833) 35560(57841) N/A N/A
Rn Rn230B 168033 131131 8210 10630 84520 N/A 23047 21822 15246(30414) 15584(30943) 12639(27478) N/A N/A
Rn Rn34A 139137 107491 79676 86235 90150 N/A 66975 64317 50478(62280) 51317(63199) 46821(58641) N/A N/A
* Value before the parenthesis is the probe count for the CORE division of ENSEMBL while value in parenthesis is the total count across all ENSEMBL divisions.

 

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