Bgee DataBase for Gene Expression Evolution

Abbreviation:Bgee

General Information

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.

Homepage http://bgee.org

Countries that developed this resource Switzerland

Created in 2008

Taxonomic range

Anolis carolinensis

Bos taurus

Caenorhabditis elegans

Drosophila melanogaster

Drosophila mojavensis

Drosophila pseudoobscura

Gorilla gorilla gorilla

Homo sapiens

Macaca mulatta

Monodelphis domestica

Mus musculus

Ornithorhynchus anatinus

Oryctolagus cuniculus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: Bgee; Bgee DataBase for Gene Expression Evolution; DOI: https://doi.org/10.25504/FAIRsharing.x6d6sx; Last edited: June 17, 2019, 11:45 a.m.; Last accessed: Jul 18 2019 10:23 a.m.

This record is maintained by marcrr ORCID

Record updated: June 17, 2019, 11:24 a.m. by marcrr.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.x6d6sx' by 'marcrr' at 11:24, 17 Jun 2019 (approved):

	'licences' has been modified:
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			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data,Software
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			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data,Software
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	'miriam_id' has been modified:
		Before: 
		After: MIR:00100541

	'tools' has been modified:
		Before:
			TopAnat - Gene Expression Enrichment||http://bgee.org/?page=top_anat#/
			BgeeDB Bioconductor|3.8|https://bioconductor.org/packages/release/bioc/html/BgeeDB.html
		After:
			TopAnat - Gene Expression Enrichment||http://bgee.org/?page=top_anat#/
			BgeeDB Bioconductor|3.8|https://bioconductor.org/packages/release/bioc/html/BgeeDB.html
			BgeeCall||http://bioconductor.org/packages/release/workflows/html/BgeeCall.html
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			BgeeCall||http://bioconductor.org/packages/release/workflows/html/BgeeCall.html
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	'organizations' has been modified:
		Before:
			BGEE administrators|http://bgee.org|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			 Etat de Vaud, Switzerland|https://www.vd.ch/|Funds
			Swiss National Science Foundation (SNSF),  Switzerland|http://www.snf.ch/fr/Pages/default.aspx|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
		After:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			 Etat de Vaud, Switzerland|https://www.vd.ch/|Funds
			Swiss National Science Foundation (SNSF),  Switzerland|http://www.snf.ch/fr/Pages/default.aspx|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
			BGEE administrators|http://bgee.org|Maintains
			University of Lausanne, department of Ecology and Evolution, Lausanne, Switzerland|https://www.unil.ch/dee/en/home.html|Maintains
		Added:
			University of Lausanne, department of Ecology and Evolution, Lausanne, Switzerland|https://www.unil.ch/dee/en/home.html|Maintains
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.x6d6sx' by 'The FAIRsharing Team' at 11:57, 15 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			BGEE administrators|http://bgee.org|Maintains
		After:
			BGEE administrators|http://bgee.org|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			 Etat de Vaud, Switzerland|https://www.vd.ch/|Funds
			Swiss National Science Foundation (SNSF),  Switzerland|http://www.snf.ch/fr/Pages/default.aspx|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
		Added:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			 Etat de Vaud, Switzerland|https://www.vd.ch/|Funds
			Swiss National Science Foundation (SNSF),  Switzerland|http://www.snf.ch/fr/Pages/default.aspx|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
		Removed:

	'related_databases' has been modified:
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			neXtProt
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			neXtProt
			ArrayExpress
			Gene Expression Omnibus
			GTEx Portal
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			ArrayExpress
			Gene Expression Omnibus
			GTEx Portal
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	'supportLinks' has been modified:
		Before:
			blog|https://bgeedb.wordpress.com/
			forum|https://github.com/BgeeDB/
			online documentation|http://bgee.unil.ch/bgee/bgee?page=documentation
			online documentation|http://bgee.org/?page=doc
			twitter|@Bgeedb
		After:
			blog|https://bgeedb.wordpress.com/
			email|Bgee@sib.swiss
			forum|https://github.com/BgeeDB/
			online documentation|http://bgee.org/?page=doc
			twitter|@Bgeedb
		Added:
			email|Bgee@sib.swiss
		Removed:
			online documentation|http://bgee.unil.ch/bgee/bgee?page=documentation

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Data Submission, Annotation and Curation
			Life Sciences
			Transcriptomics
		Added:
			Data Submission, Annotation and Curation
			Transcriptomics
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	'onto_domains' has been modified:
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			Analysis
			Gene expression data
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			Analysis
			Annotation
			Biocuration
			Differential gene expression analysis
			Gene expression data
			RNA sequence
			RNA-seq assay
			gene expression
			homologous
			in-situ hybridization assay
			orthologous
		Added:
			Annotation
			Biocuration
			Differential gene expression analysis
			RNA sequence
			RNA-seq assay
			gene expression
			homologous
			in-situ hybridization assay
			orthologous
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	'contact' has been modified:
		Before: 
		After: Frederic B. Bastian

	'contactEmail' has been modified:
		Before: Bgee@isb-sib.ch
		After: frederic.bastian@unil.ch

	'grants' has been modified:
		Before:
		After:
			31003A 133011/1
			31003A_153341
			DBI -1062350
			DBI-0641025
			DBI-1062404
			DBI-1062542
			EF-0423641
			EF-0905606
		Added:
			31003A 133011/1
			31003A_153341
			DBI -1062350
			DBI-0641025
			DBI-1062404
			DBI-1062542
			EF-0423641
			EF-0905606
		Removed:

	'publications' has been modified:
		Before:
			Uncovering hidden duplicated content in public transcriptomics data.|Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian FB., |Database (Oxford)|2013
			Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.|Haendel MA,Balhoff JP,Bastian FB,Blackburn DC,Blake JA,Bradford Y,Comte A,Dahdul WM,Dececchi TA,Druzinsky RE,Hayamizu TF,Ibrahim N,Lewis SE,Mabee PM,Niknejad A,Robinson-Rechavi M,Sereno PC,Mungall CJ|J Biomed Semantics|2014
			vHOG, a multispecies vertebrate ontology of homologous organs groups.|Niknejad A,Comte A,Parmentier G,Roux J,Bastian FB,Robinson-Rechavi M|Bioinformatics|2012
			Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species|Frederic Bastian, Gilles Parmentier, Julien Roux, Sebastien Moretti, Vincent Laudet, Marc Robinson-Rechavi|Lecture Notes in Computer Science|2008
		After:
			Uncovering hidden duplicated content in public transcriptomics data.|Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian FB., |Database (Oxford)|2013
			Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.|Haendel MA,Balhoff JP,Bastian FB,Blackburn DC,Blake JA,Bradford Y,Comte A,Dahdul WM,Dececchi TA,Druzinsky RE,Hayamizu TF,Ibrahim N,Lewis SE,Mabee PM,Niknejad A,Robinson-Rechavi M,Sereno PC,Mungall CJ|J Biomed Semantics|2014
			vHOG, a multispecies vertebrate ontology of homologous organs groups.|Niknejad A,Comte A,Parmentier G,Roux J,Bastian FB,Robinson-Rechavi M|Bioinformatics|2012
			Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species|Frederic Bastian, Gilles Parmentier, Julien Roux, Sebastien Moretti, Vincent Laudet, Marc Robinson-Rechavi|Lecture Notes in Computer Science|2008
			BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.|Komljenovic A,Roux J,Wollbrett J,Robinson-Rechavi M,Bastian FB|F1000Res|2016
		Added:
			BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.|Komljenovic A,Roux J,Wollbrett J,Robinson-Rechavi M,Bastian FB|F1000Res|2016
		Removed:

	'dataProcesses' has been modified:
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			Download
			search
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			Gene expression download
			Search
			Processed expression values
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			Gene expression download
			Search
			Processed expression values
		Removed:
			Download
			search

	'tools' has been modified:
		Before:
			TopAnat - Gene Expression Enrichment||http://bgee.org/?page=top_anat#/
		After:
			TopAnat - Gene Expression Enrichment||http://bgee.org/?page=top_anat#/
			BgeeDB Bioconductor|3.8|https://bioconductor.org/packages/release/bioc/html/BgeeDB.html
		Added:
			BgeeDB Bioconductor|3.8|https://bioconductor.org/packages/release/bioc/html/BgeeDB.html
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.x6d6sx' by 'The FAIRsharing Team' at 10:34, 15 Mar 2019 (approved):

	'taxonomies' has been modified:
		Before:
			Anolis carolinensis
			Bos taurus
			Caenorhabditis elegans
			Danio rerio
			Drosophila melanogaster
			Gallus gallus
			Gorilla gorilla gorilla
			Homo sapiens
			Macaca mulatta
			Monodelphis domestica
			Mus musculus
			Ornithorhynchus anatinus
			Pan paniscus
			Pan troglodytes
			Rattus norvegicus
			Sus scrofa
			Xenopus tropicalis
		After:
			Anolis carolinensis
			Bos taurus
			Caenorhabditis elegans
			Canis lupus
			Cavia porcellus
			Danio rerio
			Drosophila ananassae
			Drosophila melanogaster
			Drosophila mojavensis
			Drosophila pseudoobscura
			Drosophila simulans
			Drosophila virilis
			Drosophila yakuba
			Equus caballus
			Erinaceus europaeus
			Felis catus
			Gallus gallus
			Gorilla gorilla gorilla
			Homo sapiens
			Macaca mulatta
			Monodelphis domestica
			Mus musculus
			Ornithorhynchus anatinus
			Oryctolagus cuniculus
			Pan paniscus
			Pan troglodytes
			Rattus norvegicus
			Sus scrofa
			Xenopus tropicalis
		Added:
			Canis lupus
			Cavia porcellus
			Drosophila ananassae
			Drosophila mojavensis
			Drosophila pseudoobscura
			Drosophila simulans
			Drosophila virilis
			Drosophila yakuba
			Equus caballus
			Erinaceus europaeus
			Felis catus
			Oryctolagus cuniculus
		Removed:

	'miriam_id' has been modified:
		Before: None
		After:

Support

General

blog	https://bgeedb.wordpress.com/
support email	General contact
forum	https://github.com/BgeeDB/
online documentation	http://bgee.org/?page=doc
twitter	@Bgeedb

Additional Information

Contact	Frederic B. Bastian
Identifiers.org	MIR:00100541

Tools

TopAnat - Gene Expression Enrichment	http://bgee.org/?page=top_anat#/
BgeeDB Bioconductor	https://bioconductor.org/packages/release/bioc/html/BgeeDB.html	3.8
BgeeCall	http://bioconductor.org/packages/release/workflows/html/BgeeCall.html

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Applies to: Database software

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Data Access

Gene expression download	https://bgee.org/?page=download&action=expr_calls
Search	https://bgee.org/?page=gene
Processed expression values	https://bgee.org/?page=download&action=proc_values

Publications

Uncovering hidden duplicated content in public transcriptomics data.

Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian FB.,
Database (Oxford) 2013

View Paper (PubMed) View Publication

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Haendel MA,Balhoff JP,Bastian FB,Blackburn DC,Blake JA,Bradford Y,Comte A,Dahdul WM,Dececchi TA,Druzinsky RE,Hayamizu TF,Ibrahim N,Lewis SE,Mabee PM,Niknejad A,Robinson-Rechavi M,Sereno PC,Mungall CJ
J Biomed Semantics 2014

View Paper (PubMed) View Publication

vHOG, a multispecies vertebrate ontology of homologous organs groups.

Niknejad A,Comte A,Parmentier G,Roux J,Bastian FB,Robinson-Rechavi M
Bioinformatics 2012

View Paper (PubMed) View Publication

Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

Frederic Bastian, Gilles Parmentier, Julien Roux, Sebastien Moretti, Vincent Laudet, Marc Robinson-Rechavi
Lecture Notes in Computer Science 2008

View Publication

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.

Komljenovic A,Roux J,Wollbrett J,Robinson-Rechavi M,Bastian FB
F1000Res 2016

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

FASTQ Sequence and Sequence Quality Format

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by marcrr ORCID

Funds

Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute) Lead
SystemsX.ch (Government body)
Etat de Vaud, Switzerland (Government body)
Swiss National Science Foundation (SNSF), Switzerland (Government body)
National Science Foundation (NSF), USA (Government body)
The National Evolutionary Synthesis Center (NESCent), USA (Research institute)

Maintains

BGEE administrators (Consortium)
University of Lausanne, department of Ecology and Evolution, Lausanne, Switzerland (University)

Grant Number(s)

31003A 133011/1 (Swiss National Science Foundation (SNSF), Switzerland)
31003A_153341 (Swiss National Science Foundation (SNSF), Switzerland)
DBI -1062350 (National Science Foundation (NSF), USA)
DBI-0641025 (National Science Foundation (NSF), USA)
DBI-1062404 (National Science Foundation (NSF), USA)
DBI-1062542 (National Science Foundation (NSF), USA)
EF-0423641 (The National Evolutionary Synthesis Center (NESCent), USA)
EF-0905606 (The National Evolutionary Synthesis Center (NESCent), USA)

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