Abstract
The pancreatic islet is a highly specialized tissue embedded in the exocrine pancreas whose primary function is that of controlling glucose homeostasis. Thus, understanding the transcriptional control of islet-cell may help to puzzle out the pathogenesis of glucose metabolism disorders. Integrative computational analyses of transcriptomic and epigenomic data allows predicting genomic coordinates of putative regulatory elements across the genome and, decipher tissue-specific functions of the non-coding genome. We herein present the Islet Regulome Browser, a tool that allows fast access and exploration of pancreatic islet epigenomic and transcriptomic data produced by different labs worldwide. The Islet Regulome Browser is now accessible on the internet or may be installed locally. It allows uploading custom tracks as well as providing interactive access to a wealth of information including Genome-Wide Association Studies (GWAS) variants, different classes of regulatory elements, together with enhancer clusters, stretch-enhancers and transcription factor binding sites in pancreatic progenitors and adult human pancreatic islets. Integration and visualization of such data may allow a deeper understanding of the regulatory networks driving tissue-specific transcription and guide the identification of regulatory variants. We believe that such tool will facilitate the access to pancreatic islet public genomic datasets providing a major boost to functional genomics studies in glucose metabolism related traits including diabetes.
Highlights
During the last decade, the advent of high-throughput “-omics” technologies, has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenomic levels
Such publicly available maps were inferred from experimental datasets such as open chromatin and histone modification profiles, performed in adult human pancreatic islets and pancreatic progenitors. (2) “transcription factors” tracks are maps of transcription factors binding sites obtained from Chip-seq experiments performed in human adult pancreatic islets and pancreatic progenitors. (3) “SNPs” tracks include Genome-Wide Association Studies (GWAS) variants datasets associated to type 2 diabetes and
The role of the Islet Regulome Browser is to provide to the pancreatic islet community fast accessibility to processed genomic data obtained from experiments performed on the endocrine pancreatic tissue
Summary
The advent of high-throughput “-omics” technologies, has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenomic levels. Sequence databases and software analysis tools are crucial tools for molecular biologist to understand the molecular mechanisms underlying tissue-specific functions. Frameworks to access processed and integrated genomic datasets may assist, computational and non-computational scientists, to bridge this gap and provide understanding and biological interpretations to the regulatory and transcriptional complexity of the genome. In this context genome browsers are key tools in the accomplishment of this task. The UCSC Genome Browser (Speir et al, 2016), ENSEMBL (Yates et al, 2016) and NCBI’s Sequence
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