Difference between revisions of "Downloads"

Revision as of 09:43, 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:

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).

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 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 table - 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).
GENE-EVENTS table - Table relating genes to AS events.

SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.

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 =====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/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 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).