Gencode 2021

Frankish, Adam; Diekhans, Mark; Jungreis, Irwin; Lagarde, Julien; Loveland, Jane; Mudge, Jonathan M.; Sisu, Cristina; Wright, James C.; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Sala, Sílvia Carbonell; Cunningham, Fiona; Domenico, Tomás Di; Donaldson, Sarah; Fiddes, Ian T.; Girón, Carlos García; González, José M.; Grego, Tiago; Hardy, Matthew P.; Hourlier, Thibaut; Howe, Kevin; Hunt, Toby; Izuogu, Osagie; Johnson, Rory; Martin, Fergal J.; Martínez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fábio C. P.; Parker, Anne; Pei, Baikang; Pozo, Fernando Campo del; Riera, F. C.; Ruffier, Magali; Schmitt, Bianca M; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczyńska-Ratajczak, Barbara; Wolf, Magnus; Xu, Jinrui; Yang, Yu; Yates, Andy; Zerbino, Daniel R.; Zhang, Y.; Choudhary, Jyoti; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim; Kellis, M; Paten, Benedict; Tress, Michael L.; Flicek, Paul

doi:10.1093/nar/gkaa1087

Cited by 708 publications

(378 citation statements)

References 33 publications

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“…D-E. Comparison of intergenic and cis-antisense RNAs from different nascent RNA-seq methods matching with public references (GENCODE(Frankish et al , 2021), FANTOM5 enchancer(Andersson et al , 2014), NONCODE(Zhao et al , 2016)).…”

Section: Figure Ev1mentioning

confidence: 99%

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Shao

Kumar

Liedschreiber

et al. 2021

Preprint

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Unique transcriptomes define naïve, primed and paused pluripotent states in mouse embryonic stem cells. Here we perform transient transcriptome sequencing (TT-seq) to de novo define and quantify coding and non-coding transcription units (TUs) in different pluripotent states. We observe a global reduction of RNA synthesis, total RNA amount and turnover rates in ground state naïve cells (2i) and paused pluripotency (mTORi). We demonstrate that elongation velocity can be reliably estimated from TT-seq nascent RNA and RNA polymerase II occupancy and observe a transcriptome-wide attenuation of elongation velocity in the two inhibitor-induced states. We also discover a relationship between elongation velocity and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ES cells are controlled predominantly on the level of RNA synthesis, and that signaling pathways governing different pluripotent states immediately control key parameters of transcription.

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Section: Figure Ev1mentioning

confidence: 99%

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Shao

Kumar

Liedschreiber

et al. 2021

Preprint

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“…Significant window pairs were designated as representing a genetic interaction if the − log 10 P peak consisted of a single window pair, with adjacent window pairs showing decreased − log 10 P values. The genes corresponding to the interaction peak were taken as the nearest protein coding genes using GENCODE v31 (Frankish et al 2021).…”

Section: Genetic Interactionsmentioning

confidence: 99%

Cost-effective mapping of genetic interactions in mammalian cells

Smith

2021

Preprint

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Comprehensive maps of genetic interactions in mammalian cells are daunting to construct because of the large number of potential interactions, ~ 2 × 108 for protein coding genes. We previously used co-inheritance of distant genes from published radiation hybrid (RH) datasets to identify genetic interactions. However, it was necessary to combine six legacy datasets from four species to obtain adequate statistical power. Mapping resolution was also limited by the low density PCR genotyping. Here, we employ shallow sequencing of nascent human RH clones as an economical approach to constructing interaction maps. In this initial study, 15 clones were analyzed, enabling construction of a network with 225 genes and 2359 interactions (FDR < 0.05). Despite its small size, the network showed significant overlap with the previous RH network and with a protein-protein interaction network. Consumables were ≤ $50 per clone, showing that affordable, high quality genetic interaction maps are feasible in mammalian cells.

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“…Predicting the molecular consequence of a genomic variant is an essential step in interpretation and requires extensive, accurate gene annotation. There are two commonly used human gene sets: Ensembl/GENCODE (Frankish et al, 2021) and RefSeq (O'Leary et al, 2019). Both sets are generated using similar but slightly different evidence and algorithms, and so differ slightly.…”

Section: Transcript Set Selectionmentioning

confidence: 99%

Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial

Hunt

Moore

Amode

et al. 2021

Preprint

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The Ensembl Variant Effect Predictor (VEP) is a freely available, open source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequence using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as SIFT and CADD. Ensembl VEP includes filtering options to customise variant prioritisation. It is well supported and updated roughly quarterly to incorporate the latest gene, variant and phenotype association information. Ensembl VEP analysis can be performed using a highly configurable, extensible command-line tool, a Representational State Transfer (REST) application programming interface (API) and a user-friendly web interface. These access methods are designed to suit different levels of bioinformatics experience and meet different needs in terms of data size, visualisation and flexibility. In this tutorial, we will describe performing variant annotation using the Ensembl VEP web tool, which enables sophisticated analysis through a simple interface.

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Gencode 2021

Cited by 708 publications

References 33 publications

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Cost-effective mapping of genetic interactions in mammalian cells

Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial

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