Difference between revisions of "Cortex AS"
From Zhang Laboratory
| Line 5: | Line 5: | ||
</pre> | </pre> | ||
| − | *Complete list of known AS events in mouse | + | *Complete list of known AS events in mouse and mouse |
| − | *Complete list of novel AS events in mouse | + | Known AS events refers to the AS events detected in existing gene models, cDNAs and ESTs. |
| + | |||
| + | For each species, there are six BED files in the compressed package, one for each type of AS events (case: cassette exons; taca: tandem cassette exons; alt5: alternative 5' splice sites; alt3: alternative 3' splice sites; mutx: mutually exclusive exons; ire: retained introns). The coordinates are for mm10 and hg19. | ||
| + | |||
| + | In each BED file, each line is an alternative isoform, and isoforms of the same AS events have the same AS ID. Using cassette exons as an example, CA-100036521-14294-117618-117680-170683[INC][40/1][DNT] and CA-100036521-14294-117618-117680-170683[SKIP][40/1][DNT] represent the inclusion and skipping isoform of the same AS event (with the same AS ID CA-100036521-14294-117618-117680-170683). The alternative exon and flanking constitutive exons (which varies for specific types of AS events) is specified for each isoform. | ||
| + | |||
| + | |||
| + | *Complete list of known and novel AS events in mouse and human | ||
| + | |||
| + | Novel AS events refers to the AS events for which at least one isoform is detected only from RNA-Seq. The format of each file is similar to that of known AS events. | ||
| − | |||
| − | |||
*Annotation of non-redundant cassette exons in mouse | *Annotation of non-redundant cassette exons in mouse | ||
*List of prioritized non-redundant cassette exons in mouse | *List of prioritized non-redundant cassette exons in mouse | ||
Revision as of 22:16, 3 February 2015
Supplementary datasets accompanying the paper:
Yan et al. Systematic discovery of regulated and highly conserved alternative exons in the mammalian brain reveals chromatin regulators modulated by nonsense-mediated decay. Under review.
- Complete list of known AS events in mouse and mouse
Known AS events refers to the AS events detected in existing gene models, cDNAs and ESTs.
For each species, there are six BED files in the compressed package, one for each type of AS events (case: cassette exons; taca: tandem cassette exons; alt5: alternative 5' splice sites; alt3: alternative 3' splice sites; mutx: mutually exclusive exons; ire: retained introns). The coordinates are for mm10 and hg19.
In each BED file, each line is an alternative isoform, and isoforms of the same AS events have the same AS ID. Using cassette exons as an example, CA-100036521-14294-117618-117680-170683[INC][40/1][DNT] and CA-100036521-14294-117618-117680-170683[SKIP][40/1][DNT] represent the inclusion and skipping isoform of the same AS event (with the same AS ID CA-100036521-14294-117618-117680-170683). The alternative exon and flanking constitutive exons (which varies for specific types of AS events) is specified for each isoform.
- Complete list of known and novel AS events in mouse and human
Novel AS events refers to the AS events for which at least one isoform is detected only from RNA-Seq. The format of each file is similar to that of known AS events.
- Annotation of non-redundant cassette exons in mouse
- List of prioritized non-redundant cassette exons in mouse