lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
Abstract Background Long 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...
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doaj-c912b34992944c66863736a959ba4b862020-11-24T21:42:10ZengBMCBMC Genomics1471-21642017-06-0118111810.1186/s12864-017-3817-0lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasetsYixiao Gong0Hsuan-Ting Huang1Yu Liang2Thomas Trimarchi3Iannis Aifantis4Aristotelis Tsirigos5Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of MedicineDepartment of Human Genetics, Miller School of Medicine, University of MiamiDepartment of Population Health, New York University School of MedicineRegeneron Pharmaceuticals, Inc.Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of MedicineDepartment of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of MedicineAbstract Background Long 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. Result To 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. Conclusion lncRNA-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.http://link.springer.com/article/10.1186/s12864-017-3817-0lncRNAComprehensive pipelineData integrationFully automatedInteractive report |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yixiao Gong Hsuan-Ting Huang Yu Liang Thomas Trimarchi Iannis Aifantis Aristotelis Tsirigos |
spellingShingle |
Yixiao Gong Hsuan-Ting Huang Yu Liang Thomas Trimarchi Iannis Aifantis Aristotelis Tsirigos lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets BMC Genomics lncRNA Comprehensive pipeline Data integration Fully automated Interactive report |
author_facet |
Yixiao Gong Hsuan-Ting Huang Yu Liang Thomas Trimarchi Iannis Aifantis Aristotelis Tsirigos |
author_sort |
Yixiao Gong |
title |
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets |
title_short |
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets |
title_full |
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets |
title_fullStr |
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets |
title_full_unstemmed |
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets |
title_sort |
lncrna-screen: an interactive platform for computationally screening long non-coding rnas in large genomics datasets |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-06-01 |
description |
Abstract Background Long 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. Result To 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. Conclusion lncRNA-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. |
topic |
lncRNA Comprehensive pipeline Data integration Fully automated Interactive report |
url |
http://link.springer.com/article/10.1186/s12864-017-3817-0 |
work_keys_str_mv |
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