Table 1

Statistics on Transcript Pattern Variant Data presented in this work.

Human

Mouse


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


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.

Le Texier et al. BMC Bioinformatics 2006 7:169   doi:10.1186/1471-2105-7-169

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