Table 1. Target Count for Affymetrix and Custom Probe Sets |
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Species |
Chiptype |
Affy-UG1 |
Affy-ENSG2 |
Affy-Refseq2 |
UG |
Refseq |
ENSG3 |
ENST3 |
ENSE |
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Hs |
HG-U133A |
12809 |
11347 |
11929 |
12928 |
15494 |
11555 |
15812 |
19295 |
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Hs |
HG-U133B |
14569 |
6887 |
7227 |
14290 |
6245 |
5228 |
6770 |
7903 |
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Hs |
HG-U133_Plus_2 |
27776 |
15275 |
16021 |
27894 |
21440 |
16698 |
22817 |
28906 |
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Hs |
HG-U95Av2 |
7849 |
7694 |
7977 |
8778 |
10639 |
7677 |
10340 |
12859 |
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Mm |
Mouse 430_2 |
25539 |
13794 |
13976 |
23842 |
16413 |
14664 |
18788 |
22929 |
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|
Mm |
MOE 430A |
13106 |
11189 |
11615 |
12460 |
12584 |
11059 |
14263 |
17344 |
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Mm |
MOE 430B |
15433 |
5518 |
5371 |
14160 |
4626 |
4545 |
5486 |
6233 |
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Mm |
MG-U74Av2 |
7827 |
7222 |
7514 |
8073 |
7799 |
6929 |
8710 |
10600 |
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Rn |
Rat230-20 |
21586 |
3951 |
4461 |
19623 |
9380 |
7238 |
9047 |
9498 |
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Rn |
RAE230A |
12389 |
3871 |
4328 |
10913 |
7209 |
5411 |
6773 |
6888 |
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Rn |
RAE230B |
11164 |
552 |
658 |
9992 |
2538 |
2055 |
2526 |
2663 |
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Rn |
RG-U34A |
4899 |
2786 |
3077 |
4701 |
4251 |
3406 |
4529 |
6602 |
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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. |
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2. Affy-ENSG and Affy-Refseq counts are based on the latest
version of Affymetrix GeneChip annotation files from
www.affymetrix.com |
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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. |
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Table 2. Affymetrix UG Probe Sets vs. Custom UG Probe Sets |
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Species |
Chiptype |
UDID Shared |
Affymetrix Only UGID |
Custom Only UGID |
Identical Probe Sets1 |
Difference <= 3 Probes2 |
Difference >= 50%3 |
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Hs |
HG-U133A |
11538 |
1271 |
1390 |
3780 |
8001 |
1726 |
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Hs |
HG-U133B |
12296 |
2273 |
1994 |
5948 |
9453 |
1687 |
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Hs |
HG-U133_Plus_2 |
24828 |
2948 |
3066 |
9225 |
16728 |
4091 |
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Hs |
HG-U95Av2 |
7032 |
817 |
1746 |
3006 |
4889 |
1014 |
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Mm |
Mouse 430_2 |
21872 |
3667 |
1970 |
6393 |
13141 |
4312 |
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Mm |
MOE 430A |
11489 |
1617 |
971 |
3526 |
7699 |
1731 |
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Mm |
MOE 430B |
12706 |
2727 |
1454 |
4296 |
8053 |
2538 |
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Mm |
MG-U74Av2 |
6491 |
1336 |
1582 |
2175 |
4035 |
1091 |
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Rn |
Rat230-20 |
17946 |
3640 |
1677 |
6366 |
12860 |
2584 |
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Rn |
RAE230A |
10140 |
2249 |
773 |
3672 |
7820 |
1104 |
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Rn |
RAE230B |
9088 |
2076 |
904 |
3517 |
6656 |
1248 |
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Rn |
RG-U34A |
4116 |
783 |
585 |
781 |
2013 |
890 |
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1. Identical probe sets are those with identical probe contents
in Affymetrix annotation and the custome annotation. |
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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. |
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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. |
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Table 3. Affymetrix ENSG Probe Sets vs. Custom ENSG Probe Sets |
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Species |
Chiptype |
ENSG Shared |
Affymetrix Only ENSG |
Custom Only ENSG |
Identical Probe Sets1 |
Difference <= 3 Probes2 |
Difference >= 50%3 |
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Hs |
Hs133A |
10044 |
1303 |
1511 |
3038 |
6317 |
1999 |
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Hs |
Hs133B |
3857 |
3030 |
1371 |
1160 |
2060 |
1283 |
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Hs |
Hs133P |
13683 |
1592 |
3015 |
2969 |
6079 |
5010 |
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Hs |
Hs95Av2 |
6504 |
1190 |
1173 |
2416 |
4005 |
1279 |
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Mm |
Mm430 |
11455 |
2339 |
3209 |
2541 |
5545 |
3726 |
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Mm |
Mm430A |
9395 |
1794 |
1664 |
2535 |
5629 |
2070 |
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Mm |
Mm430B |
2740 |
2778 |
1805 |
759 |
1443 |
856 |
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Mm |
MmU74Av2 |
5608 |
1614 |
1321 |
1776 |
3250 |
1140 |
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Rn |
Rn230 |
2944 |
1007 |
4294 |
476 |
1468 |
1094 |
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Rn |
Rn230A |
2875 |
996 |
2536 |
516 |
1594 |
899 |
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Rn |
Rn230B |
94 |
458 |
1961 |
12 |
43 |
32 |
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Rn |
RnU34A |
2073 |
713 |
1333 |
228 |
704 |
799 |
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1. Identical probe sets are those with identical probe contents
in Affymetrix annotation and the custome annotation. |
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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. |
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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. |
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Table 4. Affymetrix Refseq Probe Sets vs. Custom Refseq Probe
Sets |
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Species |
Chiptype |
Refseq Shared |
Affymetrix Only Refseq |
Custom Only Refseq |
Identical Probe Sets1 |
Difference <= 3 Probes2 |
Difference >= 50%3 |
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Hs |
Hs133A |
9147 |
2782 |
6347 |
3044 |
6328 |
1555 |
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Hs |
Hs133B |
3646 |
3581 |
2599 |
1099 |
2054 |
1154 |
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Hs |
Hs133P |
12873 |
3148 |
8567 |
3078 |
6342 |
4496 |
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Hs |
Hs95Av2 |
5806 |
2171 |
4833 |
2061 |
3718 |
1001 |
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Mm |
Mm430 |
12188 |
1788 |
4225 |
2589 |
5954 |
4097 |
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Mm |
Mm430A |
10210 |
1405 |
2374 |
2598 |
6154 |
2306 |
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Mm |
Mm430B |
2514 |
2857 |
2112 |
686 |
1335 |
808 |
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Mm |
MmU74Av2 |
6053 |
1461 |
1746 |
1657 |
3469 |
1224 |
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Rn |
Rn230 |
3956 |
505 |
5424 |
815 |
2400 |
1082 |
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Rn |
Rn230A |
3850 |
478 |
3359 |
892 |
2591 |
796 |
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Rn |
Rn230B |
168 |
490 |
2370 |
25 |
92 |
44 |
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Rn |
RnU34A |
2724 |
353 |
1527 |
424 |
1214 |
737 |
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1. Identical probe sets are those with identical probe contents
in Affymetrix annotation and the custome annotation. |
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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. |
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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. |
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Table 5. Distribution of ENSEMBL Probe Sets in ENSEMBL CORE,
ESTGENE and VEGA Databases |
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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 |
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Table 6. Probe Utilization in Affymetrix and Custom CDF files |
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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. |
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