Table 1. Target Count for Affymetrix and Custom Probe Sets

Species Chiptype Affy-UG1 Affy-ENSG2 Affy-Refseq2 UG Refseq ENSG3 ENST3 ENSE
Hs HG-U133A 12809 11347 11929 12928 15494 11555 15812 19295
Hs HG-U133B 14569 6887 7227 14290 6245 5228 6770 7903
Hs HG-U133_Plus_2 27776 15275 16021 27894 21440 16698 22817 28906
Hs HG-U95Av2 7849 7694 7977 8778 10639 7677 10340 12859
Mm Mouse 430_2 25539 13794 13976 23842 16413 14664 18788 22929
Mm MOE 430A 13106 11189 11615 12460 12584 11059 14263 17344
Mm MOE 430B 15433 5518 5371 14160 4626 4545 5486 6233
Mm MG-U74Av2 7827 7222 7514 8073 7799 6929 8710 10600
Rn Rat230-20 21586 3951 4461 19623 9380 7238 9047 9498
Rn RAE230A 12389 3871 4328 10913 7209 5411 6773 6888
Rn RAE230B 11164 552 658 9992 2538 2055 2526 2663
Rn RG-U34A 4899 2786 3077 4701 4251 3406 4529 6602
  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 UDID Shared Affymetrix Only UGID Custom Only UGID Identical Probe Sets1 Difference <= 3 Probes2 Difference >= 50%3
Hs HG-U133A 11538 1271 1390 3780 8001 1726
Hs HG-U133B 12296 2273 1994 5948 9453 1687
Hs HG-U133_Plus_2 24828 2948 3066 9225 16728 4091
Hs HG-U95Av2 7032 817 1746 3006 4889 1014
Mm Mouse 430_2 21872 3667 1970 6393 13141 4312
Mm MOE 430A 11489 1617 971 3526 7699 1731
Mm MOE 430B 12706 2727 1454 4296 8053 2538
Mm MG-U74Av2 6491 1336 1582 2175 4035 1091
Rn Rat230-20 17946 3640 1677 6366 12860 2584
Rn RAE230A 10140 2249 773 3672 7820 1104
Rn RAE230B 9088 2076 904 3517 6656 1248
Rn RG-U34A 4116 783 585 781 2013 890
  1. Identical probe sets are those with identical probe contents in Affymetrix annotation and the custom 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 ENSG Probe Sets vs. Custom ENSG Probe Sets

Species Chiptype ENSG Shared  Affymetrix Only ENSG Custom Only ENSG Identical Probe Sets1 Difference <= 3 Probes2 Difference >= 50%3
Hs Hs133A 10044 1303 1511 3038 6317 1999
Hs Hs133B 3857 3030 1371 1160 2060 1283
Hs Hs133P 13683 1592 3015 2969 6079 5010
Hs Hs95Av2 6504 1190 1173 2416 4005 1279
Mm Mm430 11455 2339 3209 2541 5545 3726
Mm Mm430A 9395 1794 1664 2535 5629 2070
Mm Mm430B 2740 2778 1805 759 1443 856
Mm MmU74Av2 5608 1614 1321 1776 3250 1140
Rn Rn230 2944 1007 4294 476 1468 1094
Rn Rn230A 2875 996 2536 516 1594 899
Rn Rn230B 94 458 1961 12 43 32
Rn RnU34A 2073 713 1333 228 704 799
  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 Refseq Probe Sets vs. Custom Refseq Probe Sets

Species Chiptype Refseq Shared  Affymetrix Only Refseq Custom Only Refseq >Identical Probe Sets1 >Difference <= 3 Probes2 Difference >= 50%3
Hs Hs133A 9147 2782 6347 >3044 >6328 1555
Hs Hs133B 3646 3581 2599 >1099 >2054 1154
Hs Hs133P 12873 3148 8567 >3078 >6342 4496
Hs Hs95Av2 5806 2171 4833 >2061 >3718 1001
Mm Mm430 12188 1788 4225 >2589 >5954 4097
Mm Mm430A 10210 1405 2374 >2598 >6154 2306
Mm Mm430B 2514 2857 2112 >686 >1335 808
Mm MmU74Av2 6053 1461 1746 >1657 >3469 1224
Rn Rn230 3956 505 5424 >815 >2400 1082
Rn Rn230A 3850 478 3359 >892 >2591 796
Rn Rn230B 168 490 2370 >25 >92 44
Rn RnU34A 2724 353 1527 >424 >1214 737
  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. Distribution of ENSEMBL Probe Sets in ENSEMBL CORE, ESTGENE and VEGA Databases

Species Chiptype ENSEMBL Division ENSG ENST ENSE
Hs Hs133A CORE 11555 15812 19295
Hs Hs133A EST 7409 21920 14378
Hs Hs133A VEGA 3259 4945 5386
Hs Hs133B CORE 5228 6770 7903
Hs Hs133B EST 4264 9390 7413
Hs Hs133B VEGA 1636 2542 2670
Hs Hs133P CORE 16698 22817 28906
Hs Hs133P EST 11881 31564 23070
Hs Hs133P VEGA 4587 7183 8299
Hs Hs95Av2 CORE 7677 10340 12859
Hs Hs95Av2 EST 4763 13641 9557
Hs Hs95Av2 VEGA 2282 3299 3628
Mm Mm430 CORE 14664 18788 22929
Mm Mm430 EST 9506 24443 16829
Mm Mm430A CORE 11059 14263 17344
Mm Mm430A EST 6999 19025 12553
Mm Mm430B CORE 4545 5486 6233
Mm Mm430B EST 2888 6176 4507
Mm MmU74Av2 CORE 6929 8710 10600
Mm MmU74Av2 EST 4145 10994 7661
Rn Rn230 CORE 7238 9047 9498
Rn Rn230 EST 7684 12558 11848
Rn Rn230A CORE 5411 6773 6888
Rn Rn230A EST 5162 8952 7868
Rn Rn230B CORE 2055 2526 2663
Rn Rn230B EST 2804 3967 4131
Rn RnU34A CORE 3406 4529 6602
Rn RnU34A EST 2569 4614 5271

Table 6. Probe Utilization in Affymetrix and Custom CDF files

Species Chiptype AFFY Affy-UG Affy-ENSG Affy-Refseq UG REFSEQ ENSG ENST ENST3 ENSE
Hs Hs133A 246799 217181 205535 211568 185595 165567 165971(170821) 167265(172132) 143188(148048) 154430(159327)
Hs Hs133B 248336 213271 122088 127720 178849 68959 81146(86228) 81669(86753) 74104(78589) 76523(81608)
Hs Hs133P 603158 522415 371161 383838 439854 262642 274138(285530) 276188(287608) 231808(242554) 256489(267955)
Hs Hs95Av2 197695 159468 160745 165777 152448 136735 138321(142370) 139184(143250) 99998(103416) 134347(138415)
Mm Mm430 495374 421281 298389 302691 328979 199800 190663(207894) 194250(211393) 152200(181472) 176151(193002)
Mm Mm430A 248864 222639 207956 213919 178223 150802 141933(149931) 144725(152640) 113967(131147) 130422(138443)
Mm Mm430B 247610 199676 91551 89956 152757 49454 49183(58430) 49983(59234) 43924(54559) 46089(54943)
Mm Mm74Av2 196670 143322 139492 143727 121919 104693 97766(103957) 99649(105799) 71895(81029) 94281(100472)
Rn Rn230 341459 288255 63964 71400 213774 89170 59856(97403) 61245(99212) 57551(95567) 49070(86323)
Rn Rn230A 174526 158697 56517 62292 116020 66324 44540(67011) 45543(68202) 43507(66347) 36451(58912)
Rn Rn230B 168033 130504 7688 9382 98948 23077 15390(30747) 15786(31377) 14943(30340) 12741(27754)
Rn Rn34A 139137 107061 68724 74837 83977 68868 52321(64366) 53374(65543) 35270(47291) 48608(60682)

* 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.