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Statistics of Affymetrix and Custom CDF Files (Version 6)

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 DoTS-SNP Refseq-SNP EntrezG-SNP ENSG-SNP3 ENST-SNP3 ENSE-SNP3
Hs Hs133A 12767 12202 12834 11732 108251 16637 11805 11527 18600 19188 22180 11653 103614 16497 11681 11411 18431 18587
Hs Hs133Av2 12737 12202 12834 11732 108251 16637 11805 11527 18600 19188 22180 11653 103614 16497 11681 11411 18431 18587
Hs Hs133B 12728 8658 9768 9039 62183 7458 5803 5535 8252 8423 22561 8985 60701 7403 5751 5488 8194 8236
Hs Hs133P 23827 16930 19080 19707 174431 23535 17232 16609 26518 29291 54553 19591 169119 23350 17084 16471 26304 28482
Hs Hs133X 23744 16958 19050 19399 162574 23269 16941 16254 25812 26547 61035 19288 157398 23096 16804 16112 25631 26059
Hs Hs95Av2 7780 8552 8881 8113 71604 11569 8090 7833 12307 12703 12541 8071 68085 11495 8035 7780 12221 12424
Hs HsFocus 8157 8196 8431 7578 57668 11047 7730 7407 11310 10138 8732 7528 55123 10939 7630 7314 11203 9774
Mm Mm11KsubA 2111 4357 4858 4330 26200 4539 3975 3914 5254 5945 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm11KsubB 2512 2966 3412 2753 19887 3192 2727 2684 4152 5435 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm430 20485 13757 17567 18130 97598 17905 15782 15393 21809 24932 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm430A 13100 11357 12914 12080 66778 13428 11785 11516 16560 18700 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm430B 11378 5949 8650 8641 34634 5577 4937 5059 6659 7117 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm74Av2 7982 7700 8722 7708 40448 8303 7325 7218 9960 11224 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133A N/A N/A N/A 11046 N/A N/A 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 N/A N/A N/A 11046 N/A N/A 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 N/A N/A N/A 8520 N/A N/A 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 N/A N/A N/A 18639 N/A N/A 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 N/A N/A N/A 18200 N/A N/A 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 N/A N/A N/A 7680 N/A N/A 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 N/A N/A N/A 7035 N/A N/A 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 19059 3296 11062 16165 N/A 11724 10198 8656 11590 12329 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230A 11946 3226 8584 10179 N/A 8883 7693 6589 8747 8910 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230B 9470 661 4401 7406 N/A 3649 3210 2519 3398 3596 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn34A 4921 2440 4557 4517 N/A 4773 4024 3722 5374 7040 N/A N/A N/A N/A N/A N/A 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 11144 1623 588 5191 7868 1756
Hs Hs133Av2 11116 1621 616 5190 7867 1727
Hs Hs133B 7985 4743 1054 2957 4690 2100
Hs Hs133P 18399 5428 1308 5918 9453 5160
Hs Hs133X 18057 5687 1342 6570 9300 5385
Hs Hs95Av2 6779 1001 1334 3433 4807 1059
Hs HsFocus 7232 925 346 4347 6379 420
Mm Mm11KsubA 1579 532 2751 820 1115 225
Mm Mm11KsubB 1946 566 807 663 1097 421
Mm Mm430 16886 3599 1244 6952 10014 3744
Mm Mm430A 11411 1689 669 6221 8474 1542
Mm Mm430B 7638 3740 1003 2939 4562 1807
Mm Mm74Av2 6459 1523 1249 3277 4446 1076
Pt Hs133A N/A N/A 11046 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11046 N/A N/A N/A
Pt Hs133B N/A N/A 8520 N/A N/A N/A
Pt Hs133P N/A N/A 18639 N/A N/A N/A
Pt Hs133X N/A N/A 18200 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7680 N/A N/A N/A
Pt HsFocus N/A N/A 7035 N/A N/A N/A
Rn Rn230 14632 4427 1533 6334 10043 2750
Rn Rn230A 9345 2601 834 4982 7290 1192
Rn Rn230B 6453 3017 953 2578 4519 1137
Rn Rn34A 3906 1015 611 1658 2484 786

 

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 11075 1692 657 2909 7334 1811
Hs Hs133Av2 11047 1690 685 2905 7333 1780
Hs Hs133B 7943 4785 1096 1965 4484 2162
Hs Hs133P 18300 5527 1407 3474 8753 5329
Hs Hs133X 17961 5783 1438 3972 8551 5553
Hs Hs95Av2 6751 1029 1362 2102 4323 1133
Hs HsFocus 7185 972 393 2558 6079 460
Mm Mm11KsubA N/A 2111 4330 N/A N/A N/A
Mm Mm11KsubB N/A 2512 2753 N/A N/A N/A
Mm Mm430 N/A 20485 18130 N/A N/A N/A
Mm Mm430A N/A 13100 12080 N/A N/A N/A
Mm Mm430B N/A 11378 8641 N/A N/A N/A
Mm Mm74Av2 N/A 7982 7708 N/A N/A N/A
Pt Hs133A N/A N/A 11046 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11046 N/A N/A N/A
Pt Hs133B N/A N/A 8520 N/A N/A N/A
Pt Hs133P N/A N/A 18639 N/A N/A N/A
Pt Hs133X N/A N/A 18200 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7680 N/A N/A N/A
Pt HsFocus N/A N/A 7035 N/A N/A N/A
Rn Rn230 N/A 19059 16165 N/A N/A N/A
Rn Rn230A N/A 11946 10179 N/A N/A N/A
Rn Rn230B N/A 9470 7406 N/A N/A N/A
Rn Rn34A N/A 4921 4517 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 10954 1248 573 2903 6863 1932
Hs Hs133Av2 10954 1248 573 2904 6865 1929
Hs Hs133B 4908 3750 627 1138 2389 1750
Hs Hs133P 15269 1661 1340 2576 6131 5881
Hs Hs133X 14977 1981 1277 3954 7193 4781
Hs Hs95Av2 7512 1040 321 2537 4668 1209
Hs HsFocus 7211 985 196 2692 5930 549
Mm Mm11KsubA 3397 960 517 976 1955 537
Mm Mm11KsubB 2285 681 399 335 849 572
Mm Mm430 11909 1848 3484 2386 5587 3891
Mm Mm430A 9874 1483 1642 2604 6191 1785
Mm Mm430B 2904 3045 2155 716 1383 1062
Mm Mm74Av2 6242 1458 976 1728 3322 1427
Rn Rn230 1233 2063 7423 240 689 387
Rn Rn230A 1208 2018 5381 281 792 262
Rn Rn230B 45 616 2474 4 22 19
Rn Rn34A 932 1508 2790 156 427 193

 

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 9182 3652 7455 5383 7016 1217
Hs Hs133Av2 9182 3652 7455 5384 7017 1216
Hs Hs133B 4836 4932 2622 2137 2897 1476
Hs Hs133P 14171 4909 9364 5594 7388 4806
Hs Hs133X 14015 5035 9254 6835 8467 3693
Hs Hs95Av2 6071 2810 5498 3446 4541 784
Hs HsFocus 5810 2621 5237 4205 5314 239
Mm Mm11KsubA 3875 983 664 2127 2788 461
Mm Mm11KsubB 2661 751 531 1131 1545 545
Mm Mm430 15070 2497 2835 6572 8567 4465
Mm Mm430A 11408 1506 2020 6399 8279 1843
Mm Mm430B 4512 4138 1065 2092 2723 1285
Mm Mm74Av2 7107 1615 1196 3439 4614 1337
Rn Rn230 8945 2117 2779 4092 5622 2530
Rn Rn230A 7032 1552 1851 4049 5384 1215
Rn Rn230B 2409 1992 1240 971 1491 643
Rn Rn34A 3986 571 787 2197 2770 572

 

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

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 11527 18600 19188
Hs Hs133A VEGA 3918 16623 8458
Hs Hs133Av2 CORE 11527 18600 19188
Hs Hs133Av2 VEGA 3918 16623 8458
Hs Hs133B CORE 5535 8252 8423
Hs Hs133B VEGA 2245 8652 4524
Hs Hs133P CORE 16609 26518 29291
Hs Hs133P VEGA 5982 25364 13701
Hs Hs133X CORE 16254 25812 26547
Hs Hs133X VEGA 5847 23946 12389
Hs Hs95Av2 CORE 7833 12307 12703
Hs Hs95Av2 VEGA 2669 10755 5568
Hs HsFocus CORE 7407 11310 10138
Hs HsFocus VEGA 2453 9710 4257
Mm Mm11KsubA CORE 3914 5254 5945
Mm Mm11KsubB CORE 2684 4152 5435
Mm Mm430 CORE 15393 21809 24932
Mm Mm430A CORE 11516 16560 18700
Mm Mm430B CORE 5059 6659 7117
Mm Mm74Av2 CORE 7218 9960 11224
Rn Rn230 CORE 8656 11590 12329
Rn Rn230A CORE 6589 8747 8910
Rn Rn230B CORE 2519 3398 3596
Rn Rn34A CORE 3722 5374 7040

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 DoTS-SNP Refseq-SNP EntrezG-SNP ENSG-SNP4 ENST-SNP4 ENSE-SNP4 3UG 3DOTS 3REFSEQ 3ENST
Hs Hs133A 246799 220826 221623 228389 173442 214677 176366 153429 152945(159488) 170872(183473) 141431(148099) 230723 164347 202668 166726 144530 144110(150279) 161948(173873) 132591(138893) 119705 202233 129837 148753
Hs Hs133Av2 246799 220628 221671 228437 173442 214677 176366 153429 152945(159488) 170872(183473) 141431(148099) 230723 164347 202668 166726 144530 144110(150279) 161948(173873) 132591(138893) 119705 202233 129837 148753
Hs Hs133B 248336 214691 163852 180897 116720 220947 76431 64631 64869(74077) 73471(93617) 60773(69843) 236210 111987 211107 73325 61820 62038(70828) 70512(89857) 57927(66588) 88706 212886 62549 80998
Hs Hs133P 603158 528074 445423 479320 333740 530896 282272 241576 240373(259761) 271821(314184) 223387(242674) 570265 318367 505177 268548 229058 227959(246405) 259133(299692) 210888(229244) 200806 495540 194371 246375
Hs Hs133X 672804 580820 428546 462035 353017 585943 301121 255684 254261(276008) 288843(338194) 248512(270118) 634208 335649 556216 285051 241414 240101(260686) 274046(321208) 234269(254715) 200274 502985 193729 244492
Hs Hs95Av2 197695 159913 182105 186968 144182 174906 144872 129395 128821(133814) 140601(149941) 124866(129894) 185527 136644 165696 137256 122126 121625(126368) 133395(142255) 117587(122355) 86018 145702 88938 100183
Hs HsFocus 97349 92076 93999 95716 77378 88024 82763 72352 70650(72446) 78388(81615) 64488(66350) 90610 72830 82666 77809 67696 66115(67804) 73943(76972) 59959(61719) 75450 87493 81175 80274
Mm Mm11KsubA 130180 46227 101406 111885 83487 105708 80189 70158 69785(69785) 77132(77132) 68351(68351) N/A N/A N/A N/A N/A N/A N/A N/A 45765 76036 44589 44055
Mm Mm11KsubB 118480 68878 88411 98399 58766 70787 60945 51078 50512(50512) 58798(58798) 48594(48594) N/A N/A N/A N/A N/A N/A N/A N/A 28851 51797 30226 30492
Mm Mm430 495374 421831 314806 381967 293279 423576 237877 206483 211671(211671) 239743(239743) 196523(196523) N/A N/A N/A N/A N/A N/A N/A N/A 184890 389028 173851 181116
Mm Mm430A 248864 230079 208246 229352 181755 219258 174114 151801 154525(154525) 174241(174241) 142606(142606) N/A N/A N/A N/A N/A N/A N/A N/A 124741 199376 129764 133646
Mm Mm430B 247610 192786 107782 153980 111745 205047 64365 55242 57564(57564) 66066(66066) 54258(54258) N/A N/A N/A N/A N/A N/A N/A N/A 83395 195865 53143 56292
Mm Mm74Av2 196670 155649 160548 177926 124459 151672 119924 105080 105387(105387) 118222(118222) 101706(101706) N/A N/A N/A N/A N/A N/A N/A N/A 80528 122444 80478 80904
Pt Hs133A 191015 N/A N/A N/A 133542 N/A N/A N/A N/A N/A N/A 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 133542 N/A N/A N/A N/A N/A N/A 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 91072 N/A N/A N/A N/A N/A N/A 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 258366 N/A N/A N/A N/A N/A N/A 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 273240 N/A N/A N/A N/A N/A N/A 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 112218 N/A N/A N/A N/A N/A N/A 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 58889 N/A N/A N/A N/A N/A N/A 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 284438 56237 180041 191901 N/A 127621 107920 85845(85845) 95347(95347) 75205(75205) N/A N/A N/A N/A N/A N/A N/A N/A 158108 N/A 108463 85895
Rn Rn230A 174526 161095 46733 117968 115027 N/A 91002 76401 63301(63301) 70179(70179) 55384(55384) N/A N/A N/A N/A N/A N/A N/A N/A 101118 N/A 82675 65643
Rn Rn230B 168033 124333 9663 62990 77584 N/A 37126 31897 22811(22811) 25470(25470) 20124(20124) N/A N/A N/A N/A N/A N/A N/A N/A 69336 N/A 32234 23283
Rn Rn34A 139137 109869 60610 109078 88829 N/A 84988 69311 63327(63327) 70701(70701) 59737(59737) N/A N/A N/A N/A N/A N/A N/A N/A 47151 N/A 45658 42085
* 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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