Journal article Open Access
EpiRegio: Analysis and retrieval of regulatory elements linked to genes
Baumgarten Nina;
Hecker Dennis;
Karunanithi Sivarajan;
Schmidt Florian;
List Markus;
Schulz Marcel H.
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.
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.
Files
(7.1 GB)
| Name | Size | |
|---|---|---|
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CellTypeInfo.csv.gz
md5:893482b8e2ec02346408f9d0ede2aa42 |
1.0 kB | Download |
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clusterREMs_1.csv.gz
md5:945f87f088b5e0dd8566a7fd23e5c9c3 |
7.4 MB | Download |
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GeneAnnotation_1.csv.gz
md5:4fb2808ccf9b8f31bd8c29c7cfbf0a7f |
1.0 MB | Download |
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GeneExpressionBlueprint_1.csv.gz
md5:2b43a6632029c7b289f260d6950b2874 |
21.0 MB | Download |
|
GeneExpressionRoadmap_1.csv.gz
md5:77753f17fcb15518046ac296dd84cf07 |
43.1 MB | Download |
|
GenomeAnnotation_1.csv.gz
md5:83316853916b1df35f35d931d2d0c53f |
97 Bytes | Download |
|
REMActivity_1.csv.gz
md5:d4668f53c78a657d26379035f96d9ef7 |
6.9 GB | Download |
|
REMAnnotationModelScore_1.csv.gz
md5:058bcffb802579e8dbc7296b504d351f |
130.3 MB | Download |
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sampleInfo_Blueprint_1.csv.gz
md5:f5be3ba36d69cf79abb438c4305ce310 |
557 Bytes | Download |
|
sampleInfo_Roadmap_1.csv.gz
md5:f1412276ae4f5dc343b0f8930366053b |
1.1 kB | Download |
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| Views | 157 | 101 |
| Downloads | 84 | 70 |
| Data volume | 51.5 GB | 51.3 GB |
| Unique views | 133 | 92 |
| Unique downloads | 30 | 27 |
Indexed in
- Publication date:
- April 14, 2020
- DOI:
-
- Keyword(s):
- web server Epigenomics enhancer gene regulation enhancer target association
- Related identifiers:
- Compiles
- 10.5281/zenodo.3751189 (Software documentation)
- Derived from
- 10.5281/zenodo.3665990 (Journal article)
- License (for files):
- Creative Commons Attribution 4.0 International