Difference between revisions of "Downloads"
From PastDB
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=====AS events===== | =====AS events===== | ||
* [{{#var:server}}/downloads/araTha10/EVENT_INFO-araTha10.tab.gz EVENTS table] - Information about AS event coordinates and sequences. TAIR10 asssembly. | * [{{#var:server}}/downloads/araTha10/EVENT_INFO-araTha10.tab.gz EVENTS table] - Information about AS event coordinates and sequences. TAIR10 asssembly. | ||
| − | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot). | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10.tab.gz MAIN PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot). |
| − | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-40-ABIOTIC.tab.gz PSI table] - Inclusion patterns of AS events in ABIOTIC stress experiments (special dataset). | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-40-ABIOTIC-v251.tab.gz ABIOTIC PSI table] - Inclusion patterns of AS events in ABIOTIC stress experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-18-BIOTIC.tab.gz PSI table] - Inclusion patterns of AS events in BIOTIC stress experiments (special dataset). | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-18-BIOTIC-v251.tab.gz BIOTIC PSI table] - Inclusion patterns of AS events in BIOTIC stress experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-21-LIGHT.tab.gz PSI table] - Inclusion patterns of AS events in LIGHT experiments (special dataset). | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-21-LIGHT-v251.tab.gz LIGHT PSI table] - Inclusion patterns of AS events in LIGHT experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-33-SPL_FACTORS.tab.gz PSI table] - Inclusion patterns of AS events upon SPLICING FACTOR disruption (special dataset). | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10-33-SPL_FACTORS-v251.tab.gz SPL_FACTORS PSI table] - Inclusion patterns of AS events upon SPLICING FACTOR disruption (special dataset). |
=====Event features===== | =====Event features===== | ||
* [{{#var:server}}/downloads/araTha10/SPLICE_SITE_SCORES-araTha10.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons. | * [{{#var:server}}/downloads/araTha10/SPLICE_SITE_SCORES-araTha10.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons. | ||
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* [{{#var:server}}/downloads/araTha10/GENE_INFO-araTha10.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes. | * [{{#var:server}}/downloads/araTha10/GENE_INFO-araTha10.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes. | ||
* [{{#var:server}}/downloads/araTha10/EXPRESSION_TABLE-araTha10.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot). | * [{{#var:server}}/downloads/araTha10/EXPRESSION_TABLE-araTha10.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot). | ||
| − | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-40-ABIOTIC-NORM.tab.gz | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-40-ABIOTIC-NORM.tab.gz ABIOTIC EXPRESSION table] - Gene expression in ABIOTIC stress experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-18-BIOTIC-NORM.tab.gz | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-18-BIOTIC-NORM.tab.gz BIOTIC EXPRESSION table] - Gene expression in BIOTIC stress experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-21-LIGHT-NORM.tab.gz | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-21-LIGHT-NORM.tab.gz LIGHT EXPRESSION table] - Gene expression in LIGHT experiments (special dataset). |
| − | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-33-SPL_FACTORS-NORM.tab.gz | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-33-SPL_FACTORS-NORM.tab.gz SPL_FACTORS EXPRESSION table] - Gene expression upon SPLICING FACTOR disruption (special dataset). |
* [{{#var:server}}/downloads/araTha10/EVENTID_to_GENEID-araTha10.tab.gz GENE-EVENTS table] - Table relating genes to AS events. | * [{{#var:server}}/downloads/araTha10/EVENTID_to_GENEID-araTha10.tab.gz GENE-EVENTS table] - Table relating genes to AS events. | ||
=====Samples===== | =====Samples===== | ||
* [{{#var:server}}/downloads/araTha10/SAMPLE_INFO-araTha10.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database. | * [{{#var:server}}/downloads/araTha10/SAMPLE_INFO-araTha10.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database. | ||
Revision as of 09:42, 5 November 2020
From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately:
Contents
Arabidopsis thaliana
AS events
- EVENTS table - Information about AS event coordinates and sequences. TAIR10 asssembly.
- MAIN PSI table - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
- ABIOTIC PSI table - Inclusion patterns of AS events in ABIOTIC stress experiments (special dataset).
- BIOTIC PSI table - Inclusion patterns of AS events in BIOTIC stress experiments (special dataset).
- LIGHT PSI table - Inclusion patterns of AS events in LIGHT experiments (special dataset).
- SPL_FACTORS PSI table - Inclusion patterns of AS events upon SPLICING FACTOR disruption (special dataset).
Event features
- SPLICE SITES table - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
- PCR VALIDATION table - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
Protein impact
- PROTEIN IMPACT table - Effect of the AS event in the open reading frame of the transcript. Version v2.3.
- PROTEIN ISOFORMS - Mappings of events to ProteinIDs.
- DOMAINS table (PFAM) - Mappings to Pfam domains
- DOMAINS table (PROSITE) - Mappings to PROSITE domains.
- PROTEIN DISORDERED REGIONS table - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.
Genes
- GENES table - Information about gene names, descriptions, genomic coordinates and biotypes.
- EXPRESSION table - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
- ABIOTIC EXPRESSION table - Gene expression in ABIOTIC stress experiments (special dataset).
- BIOTIC EXPRESSION table - Gene expression in BIOTIC stress experiments (special dataset).
- LIGHT EXPRESSION table - Gene expression in LIGHT experiments (special dataset).
- SPL_FACTORS EXPRESSION table - Gene expression upon SPLICING FACTOR disruption (special dataset).
- GENE-EVENTS table - Table relating genes to AS events.
Samples
- SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.