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Statistics of Affymetrix and Custom CDF Files (Version 5)

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 12794 11835 12733 11839 99571 15820 11805 11453 18097 19103 22172 11750 94753 15627 11669 11328 17871 18455
Hs Hs133Av2 12757 11835 12733 11839 99571 15820 11805 11453 18097 19103 22172 11750 94753 15627 11669 11328 17871 18455
Hs Hs133B 12836 7780 9401 8976 53553 6937 5803 5474 7993 8355 22559 8926 52270 6890 5751 5428 7931 8155
Hs Hs133P 24051 16016 18928 20038 157017 22235 17232 16451 25711 29113 54540 19910 151292 22009 17072 16307 25446 28247
Hs Hs133X 23964 16041 18867 19757 146503 21842 16941 16114 24881 26393 60997 19623 142023 21617 16793 15968 24626 25855
Hs Hs95Av2 7803 8264 8816 8202 67247 11029 8090 7807 12032 12673 12538 8153 64316 10955 8030 7749 11951 12367
Hs HsFocus 8149 8181 8390 7577 54746 10479 7730 7393 11027 10122 8730 7518 51830 10346 7621 7290 10885 9732
Mm Mm430 20571 13710 17425 18722 90361 16480 15513 15060 19170 23256 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm430A 12949 11311 12820 12241 62536 12400 11657 11265 14377 17357 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm430B 11617 5830 8488 9013 31332 5028 4741 4849 5903 6627 N/A N/A N/A N/A N/A N/A N/A N/A
Mm Mm74Av2 7986 7597 8567 7784 37729 7700 7217 7000 8676 10365 N/A N/A N/A N/A N/A N/A N/A N/A
Pt Hs133A N/A N/A N/A 11102 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 11102 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 8448 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 18889 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 18461 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 7740 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 6990 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 18901 3999 11912 15982 N/A 9282 1964 8607 11374 12277 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230A 11910 3911 9081 10018 N/A 7117 1374 6555 8585 8876 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn230B 9413 795 4863 7269 N/A 2630 649 2503 3332 3577 N/A N/A N/A N/A N/A N/A N/A N/A
Rn Rn34A 4924 2940 4559 4529 N/A 4023 766 3694 5254 7011 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 11182 1612 657 4800 7647 1920
Hs Hs133Av2 11153 1604 686 4802 7649 1885
Hs Hs133B 7924 4912 1052 2799 4576 2155
Hs Hs133P 18555 5496 1483 5624 9280 5450
Hs Hs133X 18250 5714 1507 6339 9158 5673
Hs Hs95Av2 6847 956 1355 3275 4707 1153
Hs HsFocus 7216 933 361 4036 6237 481
Mm Mm430 17215 3356 1507 6487 9848 4074
Mm Mm430A 11488 1461 753 5732 8216 1694
Mm Mm430B 7866 3751 1147 2834 4652 1904
Mm Mm74Av2 6531 1455 1253 3056 4317 1217
Pt Hs133A N/A N/A 11102 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11102 N/A N/A N/A
Pt Hs133B N/A N/A 8448 N/A N/A N/A
Pt Hs133P N/A N/A 18889 N/A N/A N/A
Pt Hs133X N/A N/A 18461 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7740 N/A N/A N/A
Pt HsFocus N/A N/A 6990 N/A N/A N/A
Rn Rn230 14598 4303 1384 5899 9699 2992
Rn Rn230A 9296 2614 722 4586 7009 1354
Rn Rn230B 6379 3034 890 2453 4422 1141
Rn Rn34A 3934 990 595 1538 2352 886

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 11103 1691 736 2635 7060 1984
Hs Hs133Av2 11074 1683 765 2631 7061 1946
Hs Hs133B 7889 4947 1087 1853 4362 2220
Hs Hs133P 18447 5604 1591 3264 8520 5627
Hs Hs133X 18134 5830 1623 3801 8396 5862
Hs Hs95Av2 6815 988 1387 1972 4188 1241
Hs HsFocus 7164 985 413 2313 5887 538
Mm Mm430 N/A 20571 18722 N/A N/A N/A
Mm Mm430A N/A 12949 12241 N/A N/A N/A
Mm Mm430B N/A 11617 9013 N/A N/A N/A
Mm Mm74Av2 N/A 7986 7784 N/A N/A N/A
Pt Hs133A N/A N/A 11102 N/A N/A N/A
Pt Hs133Av2 N/A N/A 11102 N/A N/A N/A
Pt Hs133B N/A N/A 8448 N/A N/A N/A
Pt Hs133P N/A N/A 18889 N/A N/A N/A
Pt Hs133X N/A N/A 18461 N/A N/A N/A
Pt Hs95Av2 N/A N/A 7740 N/A N/A N/A
Pt HsFocus N/A N/A 6990 N/A N/A N/A
Rn Rn230 N/A 18901 15982 N/A N/A N/A
Rn Rn230A N/A 11910 10018 N/A N/A N/A
Rn Rn230B N/A 9413 7269 N/A N/A N/A
Rn Rn34A N/A 4924 4529 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 10687 1148 766 2879 6845 1726
Hs Hs133Av2 10687 1148 766 2880 6847 1723
Hs Hs133B 4555 3225 919 1106 2333 1489
Hs Hs133P 14594 1422 1857 2558 6200 5185
Hs Hs133X 14314 1727 1800 3779 6927 4510
Hs Hs95Av2 7299 965 508 2530 4670 1024
Hs HsFocus 7199 982 194 2697 5919 553
Mm Mm430 11816 1894 3244 2335 5476 4036
Mm Mm430A 9821 1490 1444 2550 6030 1971
Mm Mm430B 2752 3078 2097 685 1320 996
Mm Mm74Av2 6145 1452 855 1679 3248 1431
Rn Rn230 3121 878 5486 618 1745 1006
Rn Rn230A 3055 856 3500 709 1997 698
Rn Rn230B 134 661 2369 31 82 37
Rn Rn34A 2301 639 1393 358 1065 509

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 9072 3661 6748 2552 6149 1393
Hs Hs133Av2 9072 3661 6748 2553 6150 1392
Hs Hs133B 4658 4743 2279 1108 2508 1451
Hs Hs133P 13878 5050 8357 2631 6362 4931
Hs Hs133X 13601 5266 8241 3781 6978 4184
Hs Hs95Av2 6022 2794 5007 1962 3937 810
Hs HsFocus 5748 2642 4731 2124 4793 415
Mm Mm430 14628 2797 1852 2922 7135 4846
Mm Mm430A 11013 1807 1387 2794 6964 2130
Mm Mm430B 4379 4109 649 1050 2244 1445
Mm Mm74Av2 6843 1724 857 1650 3554 1640
Rn Rn230 8634 3278 648 1601 4677 2718
Rn Rn230A 6626 2455 491 1532 4408 1370
Rn Rn230B 2413 2450 217 420 1291 721
Rn Rn34A 3733 826 290 587 1736 743

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

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 11453 18097 19103
Hs Hs133A VEGA 3640 5850 6136
Hs Hs133Av2 CORE 11453 18097 19103
Hs Hs133Av2 VEGA 3640 5850 6136
Hs Hs133B CORE 5474 7993 8355
Hs Hs133B VEGA 1811 2848 2965
Hs Hs133P CORE 16451 25711 29113
Hs Hs133P VEGA 5112 8374 9376
Hs Hs133X CORE 16114 24881 26393
Hs Hs133X VEGA 5024 8060 8495
Hs Hs95Av2 CORE 7807 12032 12673
Hs Hs95Av2 VEGA 2553 3942 4165
Hs HsFocus CORE 7393 11027 10122
Hs HsFocus VEGA 2407 3653 3305
Mm Mm430 CORE 15060 19170 23256
Mm Mm430A CORE 11265 14377 17357
Mm Mm430B CORE 4849 5903 6627
Mm Mm74Av2 CORE 7000 8676 10365
Rn Rn230 CORE 8607 11374 12277
Rn Rn230A CORE 6555 8585 8876
Rn Rn230B CORE 2503 3332 3577
Rn Rn34A CORE 3694 5254 7011

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 220639 211296 221968 171084 184454 155536 153429 152358(157259) 152895(157726) 140886(145839) 229665 161568 173484 146350 144043 143089(147741) 144297(148906) 131651(136361) 119064 174895 117885 126883
Hs Hs133Av2 246799 220441 211344 222016 171084 184454 155536 153429 152358(157259) 152895(157726) 140886(145839) 229665 161568 173484 146350 144043 143089(147741) 144297(148906) 131651(136361) 119064 174895 117885 126883
Hs Hs133B 248336 214757 141773 166292 112952 178484 65352 64631 64518(70283) 64968(70668) 60430(66166) 235787 108179 170676 62617 61701 61576(67097) 62241(67729) 57476(62975) 87200 172482 54944 60839
Hs Hs133P 603158 527986 406025 454495 327680 427438 244291 241576 239229(251403) 240435(252432) 222303(234482) 568689 311826 406111 231587 228434 226271(237882) 228435(239943) 209307(220933) 201543 402707 175430 195071
Hs Hs133X 672804 580873 406435 454946 347372 456041 258567 255684 253011(266535) 253929(267245) 247292(260773) 632297 329417 432411 244012 240753 238285(251063) 240253(252914) 232479(245222) 201955 407820 175618 194118
Hs Hs95Av2 197695 160105 173029 181472 142976 155767 130921 129395 128563(132721) 128746(132835) 124620(128796) 184686 134960 146857 123437 121691 120978(124934) 121609(125521) 116950(120917) 86440 133310 85700 90549
Hs HsFocus 97349 91955 94181 95177 75932 77779 73262 72352 70536(72221) 70506(72158) 64378(66085) 90142 71205 72656 68447 67443 65769(67343) 66162(67709) 59639(61240) 74147 77356 71994 71039
Mm Mm430 495374 424549 305968 371193 293658 344482 201717 201156 202381(202381) 205476(205476) 187501(187501) N/A N/A N/A N/A N/A N/A N/A N/A 187893 318474 152931 158557
Mm Mm430A 248864 229266 203587 223912 180204 187405 149653 149410 148780(148780) 150929(150929) 137065(137065) N/A N/A N/A N/A N/A N/A N/A N/A 124685 172099 115105 117442
Mm Mm430B 247610 196317 103531 148585 113891 157606 52545 52279 54060(54060) 55047(55047) 50816(50816) N/A N/A N/A N/A N/A N/A N/A N/A 85872 151113 44522 47752
Mm Mm74Av2 196670 155804 156907 173491 122774 128352 103147 103107 101388(101388) 102817(102817) 97755(97755) N/A N/A N/A N/A N/A N/A N/A N/A 80653 107660 74507 74190
Pt Hs133A 191015 N/A N/A N/A 132048 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 132048 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 88155 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 254048 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 268937 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 111517 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 57884 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 283481 69007 189688 184172 N/A 91890 15904 85495(85495) 86456(86456) 74882(74882) N/A N/A N/A N/A N/A N/A N/A N/A 154355 N/A 81648 78912
Rn Rn230A 174526 160743 57710 122522 110247 N/A 68002 10925 63043(63043) 63760(63760) 55147(55147) N/A N/A N/A N/A N/A N/A N/A N/A 97951 N/A 62803 60102
Rn Rn230B 168033 123750 11598 68171 74569 N/A 24164 4913 22713(22713) 22977(22977) 20033(20033) N/A N/A N/A N/A N/A N/A N/A N/A 67298 N/A 21954 21281
Rn Rn34A 139137 109845 75329 108029 86056 N/A 67396 10804 62986(62986) 63580(63580) 59409(59409) N/A N/A N/A N/A N/A N/A N/A N/A 46843 N/A 39701 40304
* 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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