Data Exploration

Echinobase Genome and Gene Model Reports and Data

Welcome, there is a new tutorial video describing some of the data features on Echinobase.

Echinobase offers many levels of support including:

• Fully supported genomes which include genepages and gene orthology analyses
• Partially supported genomes with JBrowse and BLAST capabilities
• Datasets of JBrowse tracks for functional genomics features 
• Datasets for graphical visualization
• Datasets for download including raw datasets or processed data
• Links to datasets stored at NCBI collected for users

The Echinobase FTP directories are found from the Downloads drop down tab.

• Go to the Downloads tab -> Browse Echinobase FTP
• Here you can see 7 folders.
• Gene Page Reports have many files that we have had requests for.

The README lists the contents of the files and the order of the columns.

• GenePageGeneralInfo_AllGenes.txt contains general information on all gene pages.
• GenePageGeneralInfo_ManuallyCurated.txt contains general information on all the manually curated gene pages.
• NcbiProteinEchinobaseGene_spur.txt contains a list of NCBI S. purpuratus proteins mapped to the appropriate Echinobase genepage ID
• NcbiProteinEchinobaseGene_aplan.txt contains a list of NCBI A. planci proteins mapped to the appropriate Echinobase genepage ID
• NcbiMrnaEchinobaseGene_spur.txt contains a list of NCBI S. purpuratus mRNAs mapped to the appropriate Echinobase genepage ID.
• NcbiMrnaEchinobaseGene_aplan.txt contains a list of NCBI A. planci mRNAs mapped to the appropriate Echinobase genepage ID
• GeneGoTerms.txt contains a list of ECB-GENE IDs mapped to GO terms
• EchinobaseGeneHumanOrthologMapping.txt contains a mapping of ECB-GENEPAGE IDs and annotation to human Entrez Gene IDs
• EchinobaseGeneMouseOrthologMapping.txt contains a mapping of ECBB-GENEPAGE IDs and annotation to mouse Entrez Gene IDs
• EchinobaseGeneZebrafishOrthologMapping.txt contains a mapping of ECB-GENEPAGE IDs and annotation to zebrafish Entrez Gene IDs
• EchinobaseGenepageToGeneIdMapping.txt contains the mapping of ECB-GENEPAGE IDs, the primary identifier for a genepage to ECB-GENE IDs for individual S. purpuratus and A. planci genes.
• GeneKoTerms.txt contains a list of ECB-GENE IDs mapped to KEGG terms
• GeneExternalRef.txt contains a list of ECB-GENE IDs with external entities
  

Another frequent request is where is the GFF?

• https://download.echinobase.org/pub/Genomics/

then choose your species.

For users interested in gene expression in development the data this is available for download and also visualization.

• https://download.echinobase.org/pub/Expression/S.pur/

These Transcripts Per Embryo and Transcripts Per Million were generated by mapping transcripts to the S. purpuratus v5.0 assembly and then using the available transcript counts and time points.

• This data can be downloaded, the TPM data is graphed on the specific genepages or can be visualized using the graphing tool and then the isolated graph data downloaded as CSV or SVG.

Other files available:

• https://download.echinobase.org/pub/BLAST/  The current list of species and transcripts and proteins 
  
• https://download.echinobase.org/pub/Documents/ The White Papers from 2017 and 2022   

And on the Wiki there are links to data at other locations

• https://wiki.xenbase.org/echinowiki/index.php/Quantitative_Expression_Datasets_and_Plotting_Tools
• https://wiki.xenbase.org/echinowiki/index.php/Links_to_Additional_Echinoderm_Datasets

Our goal is to collect and provide data that is used by the Echinoderm community, please contact us if you have data or protocols or other resources that you would like to be included on Echinobase.

Thanks!