FC-R2: A comprehensive atlas of human long non-coding RNAs expression using a standardized pipeline

• Autor(a) principal: Eddie Luidy Imada
• Data de Publicação: 2019
• Tipo de documento: Tese
• Idioma: eng
• Título da fonte: Repositório Institucional da UFMG
• Texto Completo: http://hdl.handle.net/1843/30015
• topic: LncRNA; FANTOM; Recount; Database; Expression

In recent years, in depth exploration of genomes structure and function has revealed a central role for non-coding RNAs (ncRNAs) in orchestrating key biological and cellular processes through the fine tuning of gene expression regulation. Most importantly, the understanding of the role for ncRNAs has also started to emerge in human disease pathogenesis. This further speaks to the importance of an in-depth characterization of ncRNA involvement in diseases, including cancer. In this work, we have built a comprehensive atlas of gene expression, named FC-R2, across the human transcriptome containing over 100,000 genes by leveraging two publicly available resources: the FANTOM CAGE Associated Transcriptome (FANTOM-CAT), and recount2. The FANTOM-CAT is a comprehensive meta-assembly of the human transcriptome encompassing coding and non-coding genes, including promoters, enhancers, and lncRNAs. recount2 is the largest, available collection of human RNA-seq data processed and quantified using a unified pipeline, containing over 4.4 trillion reads from over 70,000 human samples from the SRA, GTEx and TCGA projects. Using FC-R2 gene expression summaries across human tissue samples from the GTEx project, we validated our approach by reproducing key findings recently described by the FANTOM consortium and the TCGA Pan-Cancer atlas. We also demonstrated the power and usability of the FC-R2 by performing two case studies in prostate cancer highlighting potential “novel” lncRNAs players involved in the clinically relevant prostate cancer phenotype. Finally, we make the FC-R2 atlas available as a public tool to empower other researchers to study important biological and clinical phenotypes and identify new candidate ncRNAs for further investigation.