European laboratories strongly contribute to develop and maintain resources — tools and databases —
about regulation of gene expression, at the genomic and epigenomic level. Relevant resources include
databases of genome annotations (Ensembl 1 , EnsemblGenomes 2 ), high-throughput functional genomics
(ArrayExpress 3 ), transcription factor binding motifs (FootprintDB 4 ; JASPAR 5 ), transcription factor binding
locations (ReMap 6 ), eukaryotic promoters (EPD 7 ), massive data generated by ENCODE 8 and
MODENCODE 9 projects, as well as specialised software suites for the analysis of cis-regulatory
sequences (Regulatory Sequence Analysis Tools 10 , i-CisTarget 11 ). These resources offer complementary
building blocks of the workflows designed by biologists and bioinformaticians to decipher regulation at the
genome scale. Their integration relies on some cumbersome pre-processing tasks to download data in
flat-file format, parse it, link and piece together information from various sources. This IS aims at providing
a software framework to extract and analyse regulatory genomics data from multiple sources, illustrated
with use cases in non-model organisms.
Author:
Contreras Moreira (on leave since 30/09/2018) , Bruno
European laboratories strongly contribute to develop and maintain resources — tools and databases —
about regulation of gene expression, at the genomic and epigenomic level. Relevant resources include
databases of genome annotations (Ensembl 1 , EnsemblGenomes 2 ), high-throughput functional genomics
(ArrayExpress 3 ), transcription factor binding motifs (FootprintDB 4 ; JASPAR 5 ), transcription factor binding
locations (ReMap 6 ), eukaryotic promoters (EPD 7 ), massive data generated by ENCODE 8 and
MODENCODE 9 projects, as well as specialised software suites for the analysis of cis-regulatory
sequences (Regulatory Sequence Analysis Tools 10 , i-CisTarget 11 ). These resources offer complementary
building blocks of the workflows designed by biologists and bioinformaticians to decipher regulation at the
genome scale. Their integration relies on some cumbersome pre-processing tasks to download data in
flat-file format, parse it, link and piece together information from various sources. This IS aims at providing
a software framework to extract and analyse regulatory genomics data from multiple sources, illustrated
with use cases in non-model organisms.