GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow,Adam Frankish,José M. González,Electra Tapanari,Mark Diekhans,Felix Kokocinski,Bronwen Aken,Daniel Barrell,Amonida Zadissa,Stephen M. J. Searle,If H. A. Barnes,Alexandra Bignell,Veronika Boychenko,Toby Hunt,M. Kay,Gaurab Mukherjee,Jeena Rajan,Gloria Despacio-Reyes,Gary Saunders,Charles A. Steward,Rachel A. Harte,Michael F. Lin,Cédric Howald,Andrea Tanzer,Thomas Derrien,Jacqueline Chrast,Nathalie Walters,Suganthi Balasubramanian,Baikang Pei,Michael L. Tress,Jose Manuel Rodriguez,Iakes Ezkurdia,Jeltje Van Baren,Michael R. Brent,David Haussler,Manolis Kellis,Alfonso Valencia,Alexandre Reymond,Mark Gerstein,Roderic Guigó,Tim Hubbard +40 more
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TLDR
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.Abstract:
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.read more
Citations
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Prognostic Impact of HOTAIR Expression is Restricted to ER-Negative Breast Cancers
TL;DR: HOTAIR appears to be a marker for lymphatic metastases rather than hematogenous metastases in ER-negative patients, and its function as a poor prognostic indicator in ER -negative patients was restricted to node-positive patients.
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FusionGDB: fusion gene annotation DataBase.
Pora Kim,Xiaobo Zhou +1 more
TL;DR: To better understand the function of FGs in cancer types and to promote the discovery of clinically relevant FGs, FusionGDB (Fusion Gene annotation DataBase) is built and provides six categories of annotations: FusionGeneSummary, FusionProtFeature, FusionGeneSequence, Fusion GenePPI, RelatedDrug and RelatedDisease.
Journal ArticleDOI
CircRNA-100338 Is Associated With mTOR Signaling Pathway and Poor Prognosis in Hepatocellular Carcinoma.
Xiu-Yan Huang,Zi-Li Huang,Ping-Bao Zhang,Xinyu Huang,Jin Huang,Hongcheng Wang,Bin Xu,Jian Zhou,Zhao-You Tang +8 more
TL;DR: Elevated circRNA-100338 activates mTOR signaling pathway in HCC via circRNAs/miR-141-3p/RHEB axis and associates with poor prognosis of hepatitis B-related HCC patients.
Journal ArticleDOI
Long noncoding RNA repertoire in chicken liver and adipose tissue.
Kévin Muret,Christophe Klopp,Valentin Wucher,Diane Esquerre,Fabrice Legeai,Frédéric Lecerf,Colette Désert,Morgane Boutin,Frédéric Jehl,Hervé Acloque,Elisabetta Giuffra,Sarah Djebali,Sylvain Foissac,Thomas Derrien,Sandrine Lagarrigue +14 more
TL;DR: An extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in theChicken.
Journal ArticleDOI
Transcriptome Analysis in Domesticated Species: Challenges and Strategies
TL;DR: Strategies for analyzing RNA-seq data are discussed, focusing particularly on questions and examples relevant to domesticated species.
References
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
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Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
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