|
|
| (13 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | From this page you can download tables with the information in VastDB. Tables are split by species, and 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: |
| − | ====Human====
| |
| − | =====AS events=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg19.tab.gz EVENTS table (hg19, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg19_ALL.tab.gz EVENTS table (hg19, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg38.tab.gz EVENTS table (hg38, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website for which genomic coordinates could be determined by LiftOver from hg19.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg38_ALL.tab.gz EVENTS table (hg38, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1) for which genomic coordinates could be determined by LiftOver from hg19.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PSI_Hsa108_hg19.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
| |
| − | =====Event features=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_SPLICE_SITE_SCORES_Hsa108_hg19.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PCR_VALIDATIONS_Hsa108_hg19.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
| |
| − | =====Protein impact=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_IMPACT_Hsa108_hg19-v1.4.2.tab.gz PROTEIN IMPACT table (VastDB)] - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_IMPACT_Hsa108_hg19_ALL-v1.4.2.tab.gz PROTEIN IMPACT table (vast-tools)] - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_PFAM_Hsa108_hg19.tab.gz DOMAINS table (PFAM)] - Mappings to Pfam domains
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_PROSITE_Hsa108_hg19.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_DISORDER_Hsa108_hg19.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_DOMAIN_PNG_URLs_Hsa108_hg19.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_STRUCT_PDB_Hsa108_hg19.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_PROT_STRUCT_PHYRE_Hsa108_hg19.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
| |
| − | =====Genes=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_GENES_Hsa108_hg19.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EXPRESSION_Hsa108_hg19.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_EVENTID_to_GENEID_Hsa108_hg19.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
| |
| − | =====Evolutionary conservation=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Mmu139_mm9.tab.gz EVENT CONSERVATION table (hg19-mm9]) - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Gga61_galGal3.tab.gz EVENT CONSERVATION table (hg19-galGal3)] - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (hg19-danRer10]) - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_GENE_HOMOLOGY_Hsa108_hg19.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
| |
| − | =====Samples=====
| |
| − | * [{{SERVER}}/downloads/Human/VASTDB_SAMPLE_INFO_Hsa108_hg19.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
| |
| − | | |
| − | ====Mouse====
| |
| − | =====AS events=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm9.tab.gz EVENTS table (mm9, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm9_ALL.tab.gz EVENTS table (mm9, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm10.tab.gz EVENTS table (mm10, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website for which genomic coordinates could be determined by LiftOver from mm9.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm10_ALL.tab.gz EVENTS table (mm10, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1) for which genomic coordinates could be determined by LiftOver from mm9.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PSI_Mmu139_mm9.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
| |
| − | =====Event features=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_SPLICE_SITE_SCORES_Mmu139_mm9.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PCR_VALIDATIONS_Mmu139_mm9.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
| |
| − | =====Protein impact=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_IMPACT_Mmu139_mm9-v1.4.2.tab.gz PROTEIN IMPACT table (VastDB)] - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_IMPACT_Mmu139_mm9_ALL-v1.4.2.tab.gz PROTEIN IMPACT table (vast-tools)] - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_PFAM_Mmu139_mm9.tab.gz DOMAINS table (PFAM)] - Mappings to Pfam domains
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_PROSITE_Mmu139_mm9.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_DISORDER_Mmu139_mm9.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_DOMAIN_PNG_URLs_Mmu139_mm9.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_STRUCT_PDB_Mmu139_mm9.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_PROT_STRUCT_PHYRE_Mmu139_mm9.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
| |
| − | =====Genes=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_GENES_Mmu139_mm9.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EXPRESSION_Mmu139_mm9.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_EVENTID_to_GENEID_Mmu139_mm9.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
| |
| − | =====Evolutionary conservation=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Hsa108_hg19.tab.gz EVENT CONSERVATION table (mm9- hg19)] - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Gga61_galGal3.tab.gz EVENT CONSERVATION table (mm9- galGal3)] - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (mm9- danRer10)] - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_GENE_HOMOLOGY_Mmu139_mm9.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
| |
| − | =====Samples=====
| |
| − | * [{{SERVER}}/downloads/Mouse/VASTDB_SAMPLE_INFO_Mmu139_mm9.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
| |
| | | | |
| − | ====Chicken==== | + | ====<i>Arabidopsis thaliana</i>==== |
| | =====AS events===== | | =====AS events===== |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_EVENTS_Gga61_galGal3.tab.gz EVENTS table (galGal3, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website. | + | * [{{#var:server}}/downloads/araTha10/EVENT_INFO-araTha10.tab.gz EVENT INFORMATION] - Information about AS event coordinates and sequences. TAIR10 asssembly. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_EVENTS_Gga61_galGal3_ALL.tab.gz EVENTS table (galGal3, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1). | + | * [{{#var:server}}/downloads/araTha10/EVENT_METRICS-araTha10.tab.gz EVENT METRICS] - Summary statistics for the usage of each AS event. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PSI_Gga61_galGal3.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages. | + | * [{{#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===== |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_SPLICE_SITE_SCORES_Gga61_galGal3.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. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PCR_VALIDATIONS_Gga61_galGal3.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===== |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_IMPACT_Gga61_galGal3-v1.4.2.tab.gz PROTEIN IMPACT table (VastDB)] - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website. | + | * [{{#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. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_IMPACT_Gga61_galGal3_ALL-v1.4.2.tab.gz PROTEIN IMPACT table (vast-tools)] - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library. | + | * [{{#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. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_PFAM_Gga61_galGal3.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. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_PROSITE_Gga61_galGal3.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. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_DISORDER_Gga61_galGal3.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons. | + | * [{{#var:server}}/downloads/araTha10/PROT_PROSITE-araTha10.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_DOMAIN_PNG_URLs_Gga61_galGal3.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
| + | * [{{#var:server}}/downloads/araTha10/PROT_DISORDER-araTha10.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3. |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_STRUCT_PDB_Gga61_galGal3.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_PROT_STRUCT_PHYRE_Gga61_galGal3.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
| |
| − | =====Genes=====
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_GENES_Gga61_galGal3.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes. | |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_EXPRESSION_Gga61_galGal3.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_EVENTID_to_GENEID_Gga61_galGal3.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
| |
| − | =====Evolutionary conservation=====
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Hsa108_hg19.tab.gz EVENT CONSERVATION table (galGal3-hg19)] - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Mmu139_mm9.tab.gz EVENT CONSERVATION table (galGal3-mm9)] - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (galGal3-danRer10)] - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_GENE_HOMOLOGY_Gga61_galGal3.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
| |
| − | =====Samples=====
| |
| − | * [{{SERVER}}/downloads/Chicken/VASTDB_SAMPLE_INFO_Gga61_galGal3.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
| |
| | | | |
| − | ====Zebrafish====
| |
| − | =====AS events=====
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTS_Dre63_danRer10.tab.gz EVENTS table (danRer10, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTS_Dre63_danRer10_ALL.tab.gz EVENTS table (danRer10, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PSI_Dre63_danRer10.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
| |
| − | =====Event features=====
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_SPLICE_SITE_SCORES_Dre63_danRer10.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PCR_VALIDATIONS_Dre63_danRer10.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
| |
| − | =====Protein impact=====
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_IMPACT_Dre63_danRer10-v1.4.2.tab.gz PROTEIN IMPACT table (VastDB)] - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website.
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_IMPACT_Dre63_danRer10_ALL-v1.4.2.tab.gz PROTEIN IMPACT table (vast-tools)] - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library.
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_PFAM_Dre63_danRer10.tab.gz DOMAINS table (PFAM)] - Mappings to Pfam domains
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_PROSITE_Dre63_danRer10.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
| |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_DISORDER_Dre63_danRer10.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
| |
| | =====Genes===== | | =====Genes===== |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_GENES_Dre63_danRer10.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. |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_EXPRESSION_Dre63_danRer10.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). |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTID_to_GENEID_Dre63_danRer10.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). |
| − | =====Evolutionary conservation=====
| + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-18-BIOTIC-NORM.tab.gz BIOTIC EXPRESSION TABLE] - Gene expression in BIOTIC stress experiments (special dataset). |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Hsa108_hg19.tab.gz EVENT CONSERVATION table (danRer10- hg19)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event. | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-21-LIGHT-NORM.tab.gz LIGHT EXPRESSION TABLE] - Gene expression in LIGHT experiments (special dataset). |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Mmu139_mm9.tab.gz EVENT CONSERVATION table (danRer10- mm9)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event. | + | * [{{#var:server}}/downloads/araTha10/cRPKM-araTha10-33-SPL_FACTORS-NORM.tab.gz SPL_FACTORS EXPRESSION TABLE] - Gene expression upon SPLICING FACTOR disruption (special dataset). |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Gga61_galGal3.tab.gz EVENT CONSERVATION table (danRer10- galGal3)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event. | + | * [{{#var:server}}/downloads/araTha10/EVENTID_to_GENEID-araTha10.tab.gz EVENT_ID-to-GENE_ID] - Table relating genes to AS events. |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_GENE_HOMOLOGY_Dre63_danRer10.tab.gz GENE HOMOLOGY table] - Homology relationships between genes. | |
| | =====Samples===== | | =====Samples===== |
| − | * [{{SERVER}}/downloads/Zebrafish/VASTDB_SAMPLE_INFO_Dre63_danRer10.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. |
From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately: