2015
DOI: 10.1093/nar/gkv1157
|View full text |Cite
|
Sign up to set email alerts
|

Ensembl 2016

Abstract: The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. W… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
3

Citation Types

6
1,330
2
8

Year Published

2016
2016
2020
2020

Publication Types

Select...
7
1

Relationship

0
8

Authors

Journals

citations
Cited by 1,344 publications
(1,346 citation statements)
references
References 47 publications
6
1,330
2
8
Order By: Relevance
“…The interaction between miRNA and murine host genes was predicted using the miRanda algorithm 3.3a [37]. Input 3ʹUTR from the M. musculus GRCm38.p4 assembly was retrieved from the Ensembl database release 86 [38]. The software was run with strict 5ʹ seed pairing, energy threshold of −20 kcal/mol and default settings for gap open and gap extend penalties.…”
Section: Methodsmentioning
confidence: 99%
“…The interaction between miRNA and murine host genes was predicted using the miRanda algorithm 3.3a [37]. Input 3ʹUTR from the M. musculus GRCm38.p4 assembly was retrieved from the Ensembl database release 86 [38]. The software was run with strict 5ʹ seed pairing, energy threshold of −20 kcal/mol and default settings for gap open and gap extend penalties.…”
Section: Methodsmentioning
confidence: 99%
“…This might especially account for newer annotations based on the recently published ENCODE project data. Therefore, we obtained alternative protein sequence datasets from Aceview (Thierry‐Mieg & Thierry‐Mieg, 2006) and Ensembl (Yates et al , 2016). Further datasets like the VEGA and GENCODE annotations are continuously integrated into Ensembl and were therefore not considered separately.…”
Section: Methodsmentioning
confidence: 99%
“…Orthologous genes in D. melanogaster for all human genes containing MXE candidates were obtained with the Ensemble BioMart service (Yates et al , 2016). This list of orthologous genes was filtered with the list of D. melanogaster genes containing MXEs, which was obtained from Hatje and Kollmar (2013), to obtain a list of genes with both types of exons, (i) MXEs in human and MXEs in D. melanogaster , and (ii) MXE candidates in human but validated to be spliced differently and MXEs in D. melanogaster .…”
Section: Methodsmentioning
confidence: 99%
“…L'épissage alternatif n'est pas une exception mais plutôt une règle puisque ce mécanisme concerne la très large majorité des gènes humains codants. Si on considère les gènes avec plusieurs exons, 90 % des gènes humains codants sont soumis à épissage alternatif [3,4]. Il y a en moyenne environ quatre transcrits différents par gène [3,4] et pour un tiers des gènes, l'épissage alternatif est à l'origine de la synthèse d'au moins cinq ARN messagers différents [3,4].…”
unclassified
“…Si on considère les gènes avec plusieurs exons, 90 % des gènes humains codants sont soumis à épissage alternatif [3,4]. Il y a en moyenne environ quatre transcrits différents par gène [3,4] et pour un tiers des gènes, l'épissage alternatif est à l'origine de la synthèse d'au moins cinq ARN messagers différents [3,4]. L'estimation de cette diversité des ARN messagers se fonde sur les connaissances actuelles, et notamment sur les bases de données de transcrits qui restent limitées : en fonction des types cellulaires et tissulaires, des stades de développement, des pathologies et des traitements appliqués (par exemple, siARN [small interfering RNA], composés chimiques, rayonnements ultra-violet, stress cytotoxique, etc.…”
unclassified