Difference between revisions of "Cortex AS"
From Zhang Laboratory
(→Complete list of known AS events) |
(→Complete list of known and novel AS events) |
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| + | {{DISPLAYTITLE:Supplementary datasets - Cortex AS}} | ||
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Supplementary datasets accompanying the paper: | Supplementary datasets accompanying the paper: | ||
<pre> | <pre> | ||
| − | Yan et al. Systematic discovery of regulated and | + | Yan et al. 2015. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A. 112:3445-3450. |
</pre> | </pre> | ||
| − | =Complete list of known AS events= | + | ==Complete list of known AS events== |
| − | download: mouse and human. | + | download: [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Mm_AS_known.bed.tgz mouse] (1.8 MB) and [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Hs_AS_known.bed.tgz human] (4.2 MB). |
Known AS events refers to the AS events detected in existing gene models, cDNAs and ESTs. | Known AS events refers to the AS events detected in existing gene models, cDNAs and ESTs. | ||
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The coordinates are for mm10 and hg19. | 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. | + | 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. | ||
| − | Note that tandem cassette | + | Note that tandem cassette exon events that involve more than two consecutive exons and retained introns were not used in analysis described in the paper. |
| − | =Complete list of | + | ==Complete list of novel AS events== |
| − | download: mouse and human | + | download: [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Mm_AS_novel.bed.tgz mouse] (13 MB) and [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Hs_AS_novel.bed.tgz human] (12 MB). |
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. | 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= | + | ==Annotation of non-redundant cassette exons== |
| − | download: mouse | + | download: [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Non_redundant_cass_mm10_summary.xlsx mouse] (17 MB) |
Spreadsheet containing a non redundant set of 13,500 known and 64,450 new cassette exons and their annotations. | Spreadsheet containing a non redundant set of 13,500 known and 64,450 new cassette exons and their annotations. | ||
| − | =List of prioritized non-redundant cassette exons= | + | ==List of prioritized non-redundant cassette exons== |
| − | download: mouse | + | download: [http://zhanglab.c2b2.columbia.edu/data/CortexAS_PNAS_2015/Non_redundant_cass_mm10_prioritized.xlsx mouse] (364 KB) |
Spreadsheet containing a combined list of 5769 non-redundant cassette exons under strong purifying selection pressure and/or cell type- and/or tissue-specific regulation. | Spreadsheet containing a combined list of 5769 non-redundant cassette exons under strong purifying selection pressure and/or cell type- and/or tissue-specific regulation. | ||
Latest revision as of 22:01, 29 March 2018
Supplementary datasets accompanying the paper:
Yan et al. 2015. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A. 112:3445-3450.
Contents
Complete list of known AS events
download: mouse (1.8 MB) and human (4.2 MB).
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.
cass: cassette exons; taca: tandem cassette exons; alt5: alternative 5' splice sites; alt3: alternative 3' splice sites; mutx: mutually exclusive exons; iret: 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.
Note that tandem cassette exon events that involve more than two consecutive exons and retained introns were not used in analysis described in the paper.
Complete list of novel AS events
download: mouse (13 MB) and human (12 MB).
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
download: mouse (17 MB)
Spreadsheet containing a non redundant set of 13,500 known and 64,450 new cassette exons and their annotations.
List of prioritized non-redundant cassette exons
download: mouse (364 KB)
Spreadsheet containing a combined list of 5769 non-redundant cassette exons under strong purifying selection pressure and/or cell type- and/or tissue-specific regulation.