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Statistics of Affymetrix and Custom CDF Files (Version 4)

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 12804 11603 12245 12008 101831 15742 11962 11605 18208 19382 22168 11923
Hs Hs133Av2 12767 11603 12245 12008 101831 15742 11962 11605 18208 19382 22168 11923
Hs Hs133B 12820 6329 6872 8892 56731 6890 5950 5581 8090 8534 22561 8848
Hs Hs133P 24068 15452 16725 20164 163929 22272 17549 16725 25929 29664 54538 20048
Hs Hs133X 23980 15500 16771 20034 154176 22065 17383 16476 25285 27008 60993 19929
Hs Hs95Av2 7810 8053 8465 8238 67995 10881 8154 7853 12055 12774 12537 8193
Hs HsFocus 8161 8113 8364 7652 55737 10432 7840 7492 11138 10266 8727 7601
Mm Mm430 20690 13164 14508 18835 95996 16313 15271 14820 18502 22858 N/A N/A
Mm Mm430A 12992 11038 11906 12168 66389 12293 11479 11090 13906 17067 N/A N/A
Mm Mm430B 11644 4646 5260 9251 32871 4935 4660 4761 5671 6506 N/A N/A
Mm Mm74Av2 8011 7297 7860 7758 39893 7597 7111 6898 8358 10195 N/A N/A
Pt Hs133A N/A N/A N/A 11306 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133Av2 N/A N/A N/A 11306 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133B N/A N/A N/A 8426 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133P N/A N/A N/A 19106 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133X N/A N/A N/A 18846 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs95Av2 N/A N/A N/A 7780 N/A N/A N/A N/A N/A N/A N/A N/A
Pt HsFocus N/A N/A N/A 7091 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230 18925 3969 4815 15860 N/A 9223 8643 7055 8759 9158 N/A N/A
Rn Rn230A 11938 3893 4575 9955 N/A 7072 6591 5276 6544 6603 N/A N/A
Rn Rn230B 9401 296 515 7150 N/A 2557 2394 2010 2475 2613 N/A N/A
Rn Rn34A 4920 2925 3345 4545 N/A 4090 3760 3261 4269 6178 N/A N

 

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 11322 1482 686 5396 8106 1787
Hs Hs133Av2 11291 1476 717 5400 8112 1747
Hs Hs133B 7808 5012 1084 3534 5064 1879
Hs Hs133P 18630 5438 1534 6950 10411 5050
Hs Hs133X 18464 5516 1570 7625 10335 5093
Hs Hs95Av2 6888 922 1350 3619 4880 1118
Hs HsFocus 7300 861 352 4421 6481 392
Mm Mm430 17383 3307 1452 6874 10123 3990
Mm Mm430A 11461 1531 707 6010 8328 1633
Mm Mm430B 8105 3539 1146 3068 4817 1919
Mm Mm74Av2 6523 1488 1235 3189 4388 1182
Pt Hs133A N/A N/A 11306 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11306 N/A N/A N/A
Pt Hs133B N/A N/A 8426 N/A N/A N/A
Pt Hs133P N/A N/A 19106 N/A N/A N/A
Pt Hs133X N/A N/A 18846 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7780 N/A N/A N/A
Pt HsFocus N/A N/A 7091 N/A N/A N/A
Rn Rn230 14541 4384 1319 5838 9649 2973
Rn Rn230A 9255 2683 700 4498 6969 1371
Rn Rn230B 6346 3055 804 2427 4373 1151
Rn Rn34A 3972 948 573 1512 2369 862

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 11250 1554 758 3015 7547 1842
Hs Hs133Av2 11220 1547 788 3014 7550 1802
Hs Hs133B 7779 5041 1113 2354 4869 1898
Hs Hs133P 18534 5534 1630 4067 9705 5164
Hs Hs133X 18375 5605 1659 4661 9540 5229
Hs Hs95Av2 6859 951 1379 2194 4389 1196
Hs HsFocus 7257 904 395 2595 6160 449
Mm Mm430 N/A 20690 18835 N/A N/A N/A
Mm Mm430A N/A 12992 12168 N/A N/A N/A
Mm Mm430B N/A 11644 9251 N/A N/A N/A
Mm Mm74Av2 N/A 8011 7758 N/A N/A N/A
Pt Hs133A N/A N/A 11306 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11306 N/A N/A N/A
Pt Hs133B N/A N/A 8426 N/A N/A N/A
Pt Hs133P N/A N/A 19106 N/A N/A N/A
Pt Hs133X N/A N/A 18846 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7780 N/A N/A N/A
Pt HsFocus N/A N/A 7091 N/A N/A N/A
Rn Rn230 N/A 18925 15860 N/A N/A N/A
Rn Rn230A N/A 11938 9955 N/A N/A N/A
Rn Rn230B N/A 9401 7150 N/A N/A N/A
Rn Rn34A N/A 4920 4545 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 10153 1450 1452 3586 7074 1424
Hs Hs133Av2 10153 1450 1452 3587 7076 1421
Hs Hs133B 4174 2155 1407 1573 2699 934
Hs Hs133P 13697 1755 3028 3597 7208 3733
Hs Hs133X 13510 1990 2966 4598 7310 3788
Hs Hs95Av2 6859 1194 994 2902 4694 851
Hs HsFocus 6941 1172 551 3236 5969 417
Mm Mm430 10566 2598 4254 2483 5448 3057
Mm Mm430A 8905 2133 2185 2493 5576 1755
Mm Mm430B 2313 2333 2448 686 1244 701
Mm Mm74Av2 5558 1739 1340 1688 3084 1168
Rn Rn230 2920 1049 4135 506 1615 878
Rn Rn230A 2848 1045 2428 523 1677 755
Rn Rn230B 95 201 1915 16 51 24
Rn Rn34A 2238 687 1023 273 818 755

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 8963 3282 6779 3304 6615 1153
Hs Hs133Av2 8963 3282 6779 3305 6616 1152
Hs Hs133B 3972 2900 2918 1490 2652 858
Hs Hs133P 12886 3839 9386 3695 7341 3444
Hs Hs133X 12776 3995 9289 4639 7311 3485
Hs Hs95Av2 5907 2558 4974 2356 4116 687
Hs HsFocus 5875 2489 4557 2728 5137 316
Mm Mm430 12430 2078 3883 2907 6736 3387
Mm Mm430A 10239 1667 2054 2770 6599 1897
Mm Mm430B 2829 2431 2106 826 1592 781
Mm Mm74Av2 6381 1479 1216 1664 3457 1370
Rn Rn230 4243 572 4980 1034 3023 634
Rn Rn230A 4036 539 3036 1039 3016 497
Rn Rn230B 317 198 2240 82 211 53
Rn Rn34A 2978 367 1112 510 1442 534

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

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 11605 18208 19382
Hs Hs133A VEGA 3522 5562 5856
Hs Hs133Av2 CORE 11605 18208 19382
Hs Hs133Av2 VEGA 3522 5562 5856
Hs Hs133B CORE 5581 8090 8534
Hs Hs133B VEGA 1796 2810 2936
Hs Hs133P CORE 16725 25929 29664
Hs Hs133P VEGA 4978 8055 9081
Hs Hs133X CORE 16476 25285 27008
Hs Hs133X VEGA 4932 7807 8287
Hs Hs95Av2 CORE 7853 12055 12774
Hs Hs95Av2 VEGA 2447 3688 3934
Hs HsFocus CORE 7492 11138 10266
Hs HsFocus VEGA 2308 3419 3130
Mm Mm430 CORE 14820 18502 22858
Mm Mm430A CORE 11090 13906 17067
Mm Mm430B CORE 4761 5671 6506
Mm Mm74Av2 CORE 6898 8358 10195
Rn Rn230 CORE 7055 8759 9158
Rn Rn230A CORE 5276 6544 6603
Rn Rn230B CORE 2010 2475 2613
Rn Rn34A CORE 3261 4269 6178

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 220727 205976 213389 177912 198884 162932 161622 160193(165392) 160512(165678) 148738(153974) 229833 168368 122906 188261 122527 131995
Hs Hs133Av2 246799 220551 206024 213437 177912 198884 162932 161622 160193(165392) 160512(165678) 148738(153974) 229833 168368 122906 188261 122527 131995
Hs Hs133B 248336 214801 104375 112086 118658 209125 69265 69914 69462(75958) 69661(76122) 65378(71855) 236004 113795 90274 201733 57754 64767
Hs Hs133P 603158 528261 358940 378068 346300 496237 259275 258786 254954(268509) 255609(269071) 238078(251643) 569145 330172 208870 465537 184053 204886
Hs Hs133X 672804 581217 393109 414929 375365 547960 279138 279050 274343(289859) 274530(289935) 268644(284127) 632712 356627 210070 475829 185364 204922
Hs Hs95Av2 197695 160297 168592 174150 145531 163444 134858 134358 133160(137425) 133408(137658) 129229(133508) 184793 137671 87162 138312 86544 91800
Hs HsFocus 97349 92076 93549 94830 78190 81879 76699 75900 73820(75478) 73928(75571) 67682(69362) 90208 73469 76329 81414 75371 74331
Mm Mm430 495374 424857 272417 291250 298782 343708 201364 199220 200144(200144) 202088(202088) 185541(185541) N/A N/A 189770 320260 152601 155313
Mm Mm430A 248864 229508 197536 207437 181007 187723 149441 148039 147210(147210) 148800(148800) 135702(135702) N/A N/A 124600 173547 114887 115380
Mm Mm430B 247610 196383 75976 85007 118201 156549 52424 51744 53425(53425) 53802(53802) 50248(50248) N/A N/A 88559 150882 44326 46563
Mm Mm74Av2 196670 155916 148051 156498 123048 128614 102871 102131 100237(100237) 101208(101208) 96672(96672) N/A N/A 80392 109091 74085 72650
Pt Hs133A 191015 N/A N/A N/A 137053 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 137053 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 92319 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 267424 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 288536 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 113605 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 59591 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 283624 56456 66378 182342 N/A 88717 84373 58545(58545) 59921(59921) 47887(47887) N/A N/A 152825 N/A 79479 56387
Rn Rn230A 174526 160996 52947 60042 109526 N/A 65751 62836 43432(43432) 44423(44423) 35440(35440) N/A N/A 96953 N/A 60951 42526
Rn Rn230B 168033 123651 3810 6703 73410 N/A 23197 21750 15188(15188) 15583(15583) 12570(12570) N/A N/A 66281 N/A 21118 14749
Rn Rn34A 139137 109829 74384 81982 87170 N/A 67000 64059 50287(50287) 51315(51315) 46621(46621) N/A N/A 47124 N/A 39573 34099
* 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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