Published April 14, 2020
| Version 0.1
Journal article
Open
EpiRegio: Analysis and retrieval of regulatory elements linked to genes
Creators
- 1. Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- 2. Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany;
- 3. Genome Institute of Singapore, 60 Biopolis Street, Genome, 02-01 Singapore 138672; Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany,
- 4. Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
Description
The data set contains all regulatory elements (REMs) and the additional information used to create the EpiRegio webserver (https://epiregio.de).
The data set consists of 10 tables (CSV-files):
- GenomeAnnotation: contains information about genomeVersion, annotationVersion and databaseName (GenomeAnnotation_1.csv.gz)
- GeneAnnotation: Information of the genes (chr, start, end, geneID, geneSymbol, alternativeGeneID, isTF, strand and annotationVersion) (GeneAnnotation_1.csv.gz)
- GeneExpression of Blueprint and Roadmap: Per consortium one table containing information about geneID, sampleID, expressionLog2TPM and species (GeneExpression_Blueprint_1.csv.gz and GeneExpressionRoadmap_1.csv.gz)
- CellTypeInfo: Information of the used cell and tissue types (cellTypeID, cellTypeName and cellOntologyTerm) (CellTypeInfo.csv.gz)
- sampleInfo of Roadmap and Blueprint: Per consortium one table containing information about sampleID, originalSampleID, cellTypeID, origin and dataType (sampleInfo_Blueprint_1.csv.gz and sampleInfo_Roadmap_1.csv.gz)
- REMAnnotation: contains all predicted REMs using STITCHIT (chr, start, end, geneID, REMID, regressionCoefficient, pValue, normModelScore, meanDNase1Signal, sdDNase1Signal, consortium and version) (REMAnnotationModelScore_1.csv.gz)
- REMActivity: This table contains per REM the DNase-signal and the standardised DNase-signal per cell or tissue type (REMID, sampleID, dnase1Log2, standDnase1Log2 and version) (REMActivity_1.csv.gz)
- clusterREMs: contains all CREMs (REMID, CREMID, chr, start, end, REMsPerCREM and version) (clusterREMs_1.csv.gz)
With these tables the underlying database of EpiRegio can easily be reconstructed. The source code for the current version of the EpiRegio webserver version is available at 10.5281/zenodo.3751189.
Notes
This work has been supported by the DZHK (German Centre for Cardiovascular Research, 81Z0200101) and the Cardio-Pulmonary Institute (CPI) [EXC 2026], and the DFG SFB/TRR 267 Noncoding RNAs in the cardiovascular system.
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Additional details
Related works
- Compiles
- Software documentation: 10.5281/zenodo.3751189 (DOI)
- Is derived from
- Journal article: 10.5281/zenodo.3665990 (DOI)