Difference between revisions of "Downloads"

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====<i>Arabidopsis thaliana</i>====
 
====<i>Arabidopsis thaliana</i>====
 
=====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 EVENT INFORMATION]  - 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.
+
* [{{#var:server}}/downloads/araTha10/EVENT_METRICS-araTha10.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.  
 +
* [{{#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-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-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-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-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 SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
−
* [{{#var:server}}/downloads/araTha10/PCR_PRIMERS-araTha10.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+
* [{{#var:server}}/downloads/araTha10/PCR_PRIMERS-araTha10.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
 
=====Protein impact=====
 
=====Protein impact=====
−
* [{{#var:server}}/downloads/araTha10/PROT_IMPACT-araTha10-v2.3.tab.gz PROTEIN IMPACT table] - Effect of the AS event in the open reading frame of the transcript. Version v2.3.
+
* [{{#var:server}}/downloads/araTha10/PROT_IMPACT-araTha10-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
−
* [{{#var:server}}/downloads/araTha10/PROT_ISOFORMS-araTha10.tab.gz PROTEIN ISOFORMS] -  Mappings of events to ProteinIDs.
+
* [{{#var:server}}/downloads/araTha10/PROT_IMPACT-araTha10-v3-legacy.tab.gz PROTEIN IMPACT (Legacy)] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3, to use with the option --legacy in vast-tools compare.  
−
* [{{#var:server}}/downloads/araTha10/PROT_PFAM-araTha10.tab.gz DOMAINS table (PFAM)] -  Mappings to Pfam domains
+
* [{{#var:server}}/downloads/araTha10/PROT_ISOFORMS-araTha10.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
−
* [{{#var:server}}/downloads/araTha10/PROT_PROSITE-araTha10.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
+
* [{{#var:server}}/downloads/araTha10/PROT_PFAM-araTha10.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
−
* [{{#var:server}}/downloads/araTha10/PROT_DISORDER-araTha10.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.
+
* [{{#var:server}}/downloads/araTha10/PROT_PROSITE-araTha10.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
 +
* [{{#var:server}}/downloads/araTha10/PROT_DISORDER-araTha10.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.
 +
 
 
=====Genes=====
 
=====Genes=====
−
* [{{#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 GENE INFORMATION] - 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.
+
* [{{#var:server}}/downloads/araTha10/EXPRESSION_TABLE-araTha10.tab.gz MAIN 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/EVENTID_to_GENEID-araTha10.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
+
* [{{#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 BIOTIC EXPRESSION TABLE] - Gene expression in BIOTIC stress experiments (special dataset).
 +
* [{{#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 SPL_FACTORS EXPRESSION TABLE] - Gene expression upon SPLICING FACTOR disruption (special dataset).
 +
* [{{#var:server}}/downloads/araTha10/EVENTID_to_GENEID-araTha10.tab.gz EVENT_ID-to-GENE_ID] - 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 INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
 +
* [{{#var:server}}/downloads/araTha10/SAMPLE_CONFIG-araTha10.tab.gz SAMPLE CONFIG PLOT] - Config file with sample information used for the plot in the main panel.

Latest revision as of 17:56, 10 October 2022

From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately:

Arabidopsis thaliana

AS events
  • EVENT INFORMATION - Information about AS event coordinates and sequences. TAIR10 asssembly.
  • EVENT METRICS - Summary statistics for the usage of each AS event.
  • 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 SITE INFORMATION - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
  • PRIMER SUGGESTIONS - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
Protein impact
Genes
Samples
  • SAMPLE INFORMATION - SRA identifiers and other information related to RNA-seq data used in this database.
  • SAMPLE CONFIG PLOT - Config file with sample information used for the plot in the main panel.
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