Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional ‘consensus’ regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the ‘total binding affinity’ of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.

Exploring functionally annotated transcriptional consensus regulatory elements with CONREL / Dalfovo, Davide; Valentini, Samuel; Romanel, Alessandro. - In: DATABASE. - ISSN 1758-0463. - 2020:(2020), pp. baaa07101-baaa0711. [10.1093/database/baaa071]

Exploring functionally annotated transcriptional consensus regulatory elements with CONREL

Dalfovo, Davide;Valentini, Samuel;Romanel, Alessandro
2020

Abstract

Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional ‘consensus’ regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the ‘total binding affinity’ of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.
Dalfovo, Davide; Valentini, Samuel; Romanel, Alessandro
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL / Dalfovo, Davide; Valentini, Samuel; Romanel, Alessandro. - In: DATABASE. - ISSN 1758-0463. - 2020:(2020), pp. baaa07101-baaa0711. [10.1093/database/baaa071]
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11572/282197
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