Difference between revisions of "Downloads"
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| − | From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately: | + | {{#vardefine:server|http://vastdb.crg.eu}}From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately: |
====<i>Arabidopsis thaliana</i>==== | ====<i>Arabidopsis thaliana</i>==== | ||
=====AS events===== | =====AS events===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/EVENT_INFO-araTha10.tab.gz EVENT INFORMATION] - Information about AS event coordinates and sequences. TAIR10 asssembly. |
| − | * [{{ | + | * [{{#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 SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons. |
| − | * [{{ | + | * [{{#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-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_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_ISOFORMS-araTha10.tab.gz PROTEIN ISOFORMS] - Mappings of events to Protein IDs. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_PFAM-araTha10.tab.gz DOMAIN OVERLAP (PFAM)] - Overlap of AS events with Pfam domains. |
| − | * [{{ | + | * [{{#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 GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes. |
| − | * [{{ | + | * [{{#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/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 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:
Contents
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
- PROTEIN IMPACT - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
- 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.
- PROTEIN ISOFORMS - Mappings of events to Protein IDs.
- DOMAIN OVERLAP (PFAM) - Overlap of AS events with Pfam domains.
- DOMAIN OVERLAP (PROSITE) - Overlap of AS events with PROSITE domains.
- PROTEIN DISORDERED REGIONS - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.
Genes
- GENE INFORMATION - Information about gene names, descriptions, genomic coordinates and biotypes.
- MAIN 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).
- EVENT_ID-to-GENE_ID - Table relating genes to AS events.
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.