Table 1 |
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Statistics on Transcript Pattern Variant Data presented in this work. |
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|
Human |
Mouse |
|
|
|
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|
Genes |
7669 |
5862 |
|
Splice patterns (& average number per gene) |
41201 (5.4) |
27132 (4.6) |
|
Transcript patterns (& average number per gene) |
12559 (1.6) |
7755 (1.3) |
|
PolyA sites as detected by AltTrans pipeline1 (& average number per gene) |
10221 (1.3) |
6976 (1.19) |
|
AltTrans polyA sites that are "skipped" |
2468 |
1113 |
|
ATD PolyA sites as detected by AltTrans and AltPAS2 pipelines (& average number per gene) |
17104 (2.2) |
9451 (1.61) |
|
ATD polyA sites that are "skipped" |
5459 |
2214 |
|
Genes showing splice events (as seen among the splice patterns) |
5672 (74%) |
3825 (65%) |
|
Genes showing multiple polyA sites (considering the polyA sites from both AltTrans and AltPAS)3 |
4603 (60%) |
2456 (42%) |
|
Genes showing both splice events and multiple polyA sites (considering the polyA sites from both AltTrans and AltPAS) |
3523 (46%) |
1718 (29%) |
|
Genes showing multiple polyA sites (considering only the AltTrans polyA sites)4 |
2053 (27%) |
1026 (18%) |
|
Genes showing both splice events and polyA events (considering only the AltTrans polyA sites) |
1679 (22%) |
736 (13%) |
|
Genes showing >= 2 Splice Patterns |
6859 |
4989 |
|
Genes showing >= 2 Transcript patterns |
3179 |
1548 |
|
EST/mRNA sequences confirming Splice Patterns |
837828 |
726916 |
|
EST/mRNA sequences confirming Transcript Patterns |
38731 |
18045 |
|
|
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1:AltTrans pipeline requires for a transcript pattern that the underlying splicing and the terminating polyA site are confirmed by the same set of EST./mRNA sequences. 2:AltPAS pipeline identifies polyA sites independent of the underlying splicing pattern. 3:A gene is considered as undergoing alternative polyadenylation if it multiple polyA sites (from the merged list of AltTrans and AltPAS polyA sites) are seen mapped to the gene. 4:Consideration of only the AltTrans polyA sites gives a conservative estimate for the extent of alternative polyadenylation. AltTrans polyA sites differ from AltPAS sites in the manner they are detected; AltTrans polyA sites are confirmed by the same set of EST/mRNA sequences that confirm the splice structure of transcript pattern. |
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Le Texier et al. BMC Bioinformatics 2006 7:169 doi:10.1186/1471-2105-7-169 |
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