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
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Journal ArticleDOI
Identification of copy number variants from exome sequence data.
Pubudu S. Samarakoon,Pubudu S. Samarakoon,Hanne Sørmo Sorte,Hanne Sørmo Sorte,Bjørn Evert Kristiansen,Tove Skodje,Ying Sheng,Geir E. Tjønnfjord,Geir E. Tjønnfjord,Barbro Stadheim,Asbjørg Stray-Pedersen,Asbjørg Stray-Pedersen,Asbjørg Stray-Pedersen,Olaug K. Rødningen,Robert Lyle,Robert Lyle +15 more
TL;DR: A protocol to detect exonic CNVs (including shorter CNVs that cover 1–4 exons), combining computational prediction algorithms and a high-resolution custom CGH array is proposed.
Journal ArticleDOI
Long non-coding RNA (LncRNA) RMST in triple-negative breast cancer (TNBC): Expression analysis and biological roles research
TL;DR: RMST played a role of tumor suppressor in TNBC through inhibiting cell proliferation, invasion and migration, enhancing cell apoptosis, and regulating cell cycle, which showed that lncRNA RMST was differentially expressed in cervical cancer.
Journal ArticleDOI
The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts
TL;DR: ZFC3H1 is established as a central nuclear pA+ RNA retention factor, counteracting nuclear export activity, in mammals with promiscuously transcribed genomes.
Journal ArticleDOI
DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.
TL;DR: DC3 (De-Convolution and Coupled-Clustering) as a method for the joint analysis of various bulk and single-cell data such as HiChIP, RNA-seq and ATAC-seq from the same heterogeneous cell population provides a comprehensive characterization of the gene regulatory system in each subpopulation.
Journal ArticleDOI
IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies
Matthias Friedrich,Mathilde Pohin,Matthew A. Jackson,Ilya Korsunsky,Samuel J. Bullers,Kevin Rue-Albrecht,Z Christoforidou,D Sathananthan,T Thomas,R Ravindran,R Tandon,R S Peres,Hannah Sharpe,Kevin Wei,Watts Gfm.,Elizabeth H. Mann,Alessandra Geremia,Moustafa Attar,Moustafa Attar,F Barone,M Brenner,Christopher D. Buckley,M Coles,A P Frei,K G Lassen,Fiona Powrie,Sarah McCuaig,L Thomas,E Collantes,Holm H. Uhlig,Stephen N. Sansom,Alistair Easton,Soumya Raychaudhuri,Simon Travis +33 more
TL;DR: In this article, the authors identify coexpressed gene modules within the heterogeneous tissular inflammatory response in IBD that map to distinct histopathological and cellular features (pathotypes), defined by high neutrophil infiltration, activation of fibroblasts and vascular remodeling at sites of deep ulceration.
References
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