lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets

BMC Genomics

Software

Hsuan-Ting Huang¹  Iannis Aifantis²  Yixiao Gong²  Aristotelis Tsirigos³  Yu Liang⁴  Thomas Trimarchi⁵ 

[1] Department of Human Genetics, Miller School of Medicine, University of Miami, 33136, Coral Gables, FL, USA;Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, 10016, New York, NY, USA;NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, New York University School of Medicine, 10016, New York, NY, USA;Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, 10016, New York, NY, USA;NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, New York University School of Medicine, 10016, New York, NY, USA;Applied Bioinformatics Laboratories, New York University School of Medicine, 10016, New York, NY, USA;Department of Population Health, New York University School of Medicine, 10016, New York, NY, USA;Regeneron Pharmaceuticals, Inc., 10591, Tarrytown, NY, USA;

关键词: lncRNA;    Comprehensive pipeline;    Data integration;    Fully automated;    Interactive report;   

DOI  :  10.1186/s12864-017-3817-0

 received in 2017-01-23, accepted in 2017-05-24,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundLong non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successful in identifying candidate lncRNAs. However, the complexity of handling and integrating different types of genomics data poses significant challenges to experimental laboratories that lack extensive genomics expertise.ResultTo address this issue, we have developed lncRNA-screen, a comprehensive pipeline for computationally screening putative lncRNA transcripts over large multimodal datasets. The main objective of this work is to facilitate the computational discovery of lncRNA candidates to be further examined by functional experiments. lncRNA-screen provides a fully automated easy-to-run pipeline which performs data download, RNA-seq alignment, assembly, quality assessment, transcript filtration, novel lncRNA identification, coding potential estimation, expression level quantification, histone mark enrichment profile integration, differential expression analysis, annotation with other type of segmented data (CNVs, SNPs, Hi-C, etc.) and visualization. Importantly, lncRNA-screen generates an interactive report summarizing all interesting lncRNA features including genome browser snapshots and lncRNA-mRNA interactions based on Hi-C data.ConclusionlncRNA-screen provides a comprehensive solution for lncRNA discovery and an intuitive interactive report for identifying promising lncRNA candidates. lncRNA-screen is available as open-source software on GitHub.

【 授权许可】

CC BY   
© The Author(s). 2017