EpiRegio: Analysis and retrieval of regulatory elements linked to genes

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. EpiRegio uses the STITCHIT algorithm, which is currently under revision.  The preprint is available at http://dx.doi.org/10.1101/585125.