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Statistics of Affymetrix and Custom CDF Files (Version 3)

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 12752 11362 11906 12666 101630 15703 2825 2516 18127 3943 22168 12522
Hs Hs133Av2 12712 11362 11906 12666 101630 15703 2825 2516 18127 3943 22168 12522
Hs Hs133B 12859 6170 6637 9022 56593 6871 1682 1357 8110 1912 22561 8972
Hs Hs133P 24373 15250 16345 21207 163567 22216 4615 3949 25851 6306 54538 21021
Hs Hs133X 24289 15282 16389 20977 153885 22010 4499 3841 25218 5828 60993 20812
Hs Hs95Av2 7831 7900 8259 8700 67893 10856 1919 1692 11984 2661 12537 8628
Hs HsFocus 8151 7915 8141 7967 55626 10402 1746 1569 11071 2115 8727 7882
Mm Mm430 20768 13030 14245 20383 95996 16313 15271 14820 18664 22858 N/A N/A
Mm Mm430A 12989 10900 11681 13241 66389 12293 11479 11090 14025 17067 N/A N/A
Mm Mm430B 11758 4466 5027 9717 32871 4935 4660 4761 5718 6506 N/A N/A
Mm Mm74Av2 8014 7221 7726 8552 39893 7597 7111 6898 8430 10195 N/A N/A
Pt Hs133A N/A N/A N/A 11303 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133Av2 N/A N/A N/A 11303 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133B N/A N/A N/A 8380 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133P N/A N/A N/A 19205 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133X N/A N/A N/A 18979 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs95Av2 N/A N/A N/A 7779 N/A N/A N/A N/A N/A N/A N/A N/A
Pt HsFocus N/A N/A N/A 7087 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230 20342 3851 4567 17103 N/A 9223 8643 7055 8759 9158 N/A N/A
Rn Rn230A 12007 3773 4358 10191 N/A 7072 6591 5276 6544 6603 N/A N/A
Rn Rn230B 10351 300 480 8035 N/A 2557 2394 2010 2475 2613 N/A N/A
Rn Rn34A 4859 2804 3159 5323 N/A 4090 3760 3261 4269 6178 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 11316 1436 1350 4968 7810 2301
Hs Hs133Av2 11284 1428 1382 4963 7808 2267
Hs Hs133B 7786 5073 1236 3363 4957 2028
Hs Hs133P 18782 5591 2425 6516 10230 5716
Hs Hs133X 18618 5671 2359 7274 10194 5671
Hs Hs95Av2 6894 937 1806 3381 4771 1400
Hs HsFocus 7318 833 649 4109 6277 675
Mm Mm430 17463 3305 2920 5637 9613 4917
Mm Mm430A 11517 1472 1724 4807 7862 2349
Mm Mm430B 8141 3617 1576 2764 4722 2152
Mm Mm74Av2 6533 1481 2019 2666 4006 1670
Pt Hs133A N/A N/A 11303 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11303 N/A N/A N/A
Pt Hs133B N/A N/A 8380 N/A N/A N/A
Pt Hs133P N/A N/A 19205 N/A N/A N/A
Pt Hs133X N/A N/A 18979 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7779 N/A N/A N/A
Pt HsFocus N/A N/A 7087 N/A N/A N/A
Rn Rn230 15201 5141 1902 5528 10093 3234
Rn Rn230A 9069 2938 1122 3702 6596 1613
Rn Rn230B 7098 3253 937 2661 4919 1299
Rn Rn34A 3971 888 1352 1185 2072 1325
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 11194 1558 1472 2780 7281 2297
Hs Hs133Av2 11163 1549 1503 2774 7276 2265
Hs Hs133B 7751 5108 1271 2244 4748 2040
Hs Hs133P 18626 5747 2581 3871 9521 5737
Hs Hs133X 18473 5816 2504 4480 9424 5730
Hs Hs95Av2 6848 983 1852 2062 4265 1454
Hs HsFocus 7244 907 723 2410 5967 701
Mm Mm430 N/A 20768 20383 N/A N/A N/A
Mm Mm430A N/A 12989 13241 N/A N/A N/A
Mm Mm430B N/A 11758 9717 N/A N/A N/A
Mm Mm74Av2 N/A 8014 8552 N/A N/A N/A
Pt Hs133A N/A N/A 11303 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11303 N/A N/A N/A
Pt Hs133B N/A N/A 8380 N/A N/A N/A
Pt Hs133P N/A N/A 19205 N/A N/A N/A
Pt Hs133X N/A N/A 18979 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7779 N/A N/A N/A
Pt HsFocus N/A N/A 7087 N/A N/A N/A
Rn Rn230 N/A 20342 17103 N/A N/A N/A
Rn Rn230A N/A 12007 10191 N/A N/A N/A
Rn Rn230B N/A 10351 8035 N/A N/A N/A
Rn Rn34A N/A 4859 5323 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 1853 9509 663 574 1200 346
Hs Hs133Av2 1853 9509 663 574 1200 346
Hs Hs133B 733 5437 624 279 473 166
Hs Hs133P 2529 12721 1420 641 1321 729
Hs Hs133X 2478 12804 1363 854 1358 720
Hs Hs95Av2 1236 6664 456 473 791 195
Hs HsFocus 1262 6653 307 540 1046 101
Mm Mm430 10506 2524 4314 2587 5646 2703
Mm Mm430A 8831 2069 2259 2521 5587 1616
Mm Mm430B 2390 2076 2371 749 1343 646
Mm Mm74Av2 5525 1696 1373 1690 3080 1142
Rn Rn230 2843 1008 4212 504 1583 854
Rn Rn230A 2771 1002 2505 520 1644 732
Rn Rn230B 96 204 1914 16 51 23
Rn Rn34A 2155 649 1106 267 798 720

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 8729 3177 6974 3243 6469 1112
Hs Hs133Av2 8729 3177 6974 3244 6470 1111
Hs Hs133B 3886 2751 2985 1454 2596 822
Hs Hs133P 12563 3782 9653 3691 7337 3171
Hs Hs133X 12439 3950 9571 4652 7306 3226
Hs Hs95Av2 5765 2494 5091 2300 4018 675
Hs HsFocus 5720 2421 4682 2670 5023 301
Mm Mm430 12227 2018 4086 2833 6547 3376
Mm Mm430A 10081 1600 2212 2656 6332 2007
Mm Mm430B 2781 2246 2154 821 1576 748
Mm Mm74Av2 6252 1474 1345 1622 3360 1397
Rn Rn230 4035 532 5188 955 2820 673
Rn Rn230A 3854 504 3218 969 2840 524
Rn Rn230B 278 202 2279 67 179 50
Rn Rn34A 2818 341 1272 482 1355 530

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

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 2516 18127 3943
Hs Hs133A VEGA 521 5558 760
Hs Hs133Av2 CORE 2516 18127 3943
Hs Hs133Av2 VEGA 521 5558 760
Hs Hs133B CORE 1357 8110 1912
Hs Hs133B VEGA 259 2811 370
Hs Hs133P CORE 3949 25851 6306
Hs Hs133P VEGA 774 8051 1181
Hs Hs133X CORE 3841 25218 5828
Hs Hs133X VEGA 764 7808 1102
Hs Hs95Av2 CORE 1692 11984 2661
Hs Hs95Av2 VEGA 386 3685 561
Hs HsFocus CORE 1569 11071 2115
Hs HsFocus VEGA 335 3410 424
Mm Mm430 CORE 14820 18664 22858
Mm Mm430 EST 8722 15232 13478
Mm Mm430A CORE 11090 14025 17067
Mm Mm430A EST 6423 11317 9812
Mm Mm430B CORE 4761 5718 6506
Mm Mm430B EST 2541 4231 3783
Mm Mm74Av2 CORE 6898 8430 10195
Mm Mm74Av2 EST 3549 6048 5801
Rn Rn230 CORE 7055 8759 9158
Rn Rn230 EST 7572 12316 11559
Rn Rn230A CORE 5276 6544 6603
Rn Rn230A EST 5076 8761 7651
Rn Rn230B CORE 2010 2475 2613
Rn Rn230B EST 2774 3911 4057
Rn Rn34A CORE 3261 4269 6178
Rn Rn34A EST 2503 4446 5004

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 3UG 3DOTS 3REFSEQ 3ENST
Hs Hs133A 246799 220151 200309 206882 179432 198443 162556 32762 30603(31379) 159720(164954) 28271(29039) 229833 169726 124752 187661 122212 131366
Hs Hs133Av2 246799 219942 200357 206930 179432 198443 162556 32762 30603(31379) 159720(164954) 28271(29039) 229833 169726 124752 187661 122213 131359
Hs Hs133B 248336 214867 100670 107292 117132 208799 69072 15918 14074(14893) 69396(75799) 13277(14084) 236004 112322 90226 201380 57577 64480
Hs Hs133P 603158 532008 342471 358779 347434 495180 258606 55371 50175(52027) 254548(267937) 46711(48542) 569145 331137 212889 464254 183537 203939
Hs Hs133X 672804 585934 372797 391392 376238 546720 278255 62386 56296(58462) 273218(288526) 55052(57216) 632712 357412 214277 474687 184827 203836
Hs Hs95Av2 197695 160487 164715 169569 147150 163109 134588 27511 25811(26543) 132766(137015) 24997(25725) 184793 139158 89162 137920 86345 91333
Hs HsFocus 97349 91988 91406 92676 78515 81664 76478 15441 14538(14772) 73488(75173) 13264(13503) 90208 73707 76664 81187 75142 73933
Mm Mm430 495374 425143 267593 284939 301396 343708 201364 199220 200144(210127) 203559(213991) 185541(195099) N/A N/A 195583 320237 152614 181495
Mm Mm430A 248864 229486 197850 207419 182263 187723 149441 148039 147210(150887) 149815(153790) 135702(139309) N/A N/A 128008 173520 114897 130774
Mm Mm430B 247610 196691 70789 78674 119428 156549 52424 51744 53425(59728) 54254(60708) 50248(56198) N/A N/A 90295 150891 44331 55520
Mm Mm74Av2 196670 156043 147402 155445 124353 128614 102871 102131 100237(103332) 101955(105289) 96672(99713) N/A N/A 84102 109111 74087 79921
Pt Hs133A 191015 N/A N/A N/A 136368 N/A N/A N/A N/A 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 136368 N/A N/A N/A N/A 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 90822 N/A N/A N/A N/A 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 265765 N/A N/A N/A N/A 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 286620 N/A N/A N/A N/A 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 113232 N/A N/A N/A N/A 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 59324 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230 341459 289069 55021 63491 184494 N/A 88717 84373 58545(95626) 59921(97408) 47887(84662) N/A N/A 158245 N/A 79481 93917
Rn Rn230A 174526 158829 51468 57485 105872 N/A 65751 62836 43432(65663) 44423(66831) 35440(57648) N/A N/A 94508 N/A 60953 65091
Rn Rn230B 168033 131230 3794 6302 79272 N/A 23197 21750 15188(30314) 15583(30942) 12570(27358) N/A N/A 72866 N/A 21118 29934
Rn Rn34A 139137 107555 71471 77881 88969 N/A 67000 64059 50287(62039) 51315(63197) 46621(58393) N/A N/A 51188 N/A 39574 45815

 

* 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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