Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species

By Frédéric B. Bastian, Gilles Parmentier, Julien Roux, S. Moretti, V. Laudet, Marc Robinson-Rechavi. 2008

189 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, background): “First, we now provide cross-references to additional resources, including STRING (18), Bgee (17) and Swiss-Model (19).”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, unknown): “Anatomy–expresses–Gene edges were extracted from Bgee and TISSUES ( Santos et al., 2015 ; Himmelstein and Jensen, 2015g ; Himmelstein and Jensen, 2015h ).”
A benchmark of gene expression tissue-specificity metrics (2015, methodology): “…project (The ENCODE Project Consortium 2011; Lin et al. 2014) as used in Kryuchkova-Mostacci & Robinson-Rechavi (Kryuchkova-Mostacci & Robinson-Rechavi 2015), and 8 human tissues and 6 mouse tissues from Brawand et al. (Brawand et al. 2011), as processed in the Bgee database (Bastian et al. 2008).”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “org) (47), a database for gene expression evolution, has grown from 5 to 17 animal species in the last 12 months, with the notable addition of a wealth of RNAseq and Affymetrix microarray gene expression data.”
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors (2018, background): “(33) and bgee database (34) of 22 animal species as well as the human protein expressions from Human Protein Map (35).”
UniProt: the universal protein knowledgebase in 2021 (2020, methodology): “…of UniProtKB sequences and annotations imported and mapped from large-scale data imports (29), and the SPARQL API that allows users to perform complex queries across all UniProt data and also other resources that provide a SPARQL endpoint, such as DisGeNET (45), Bgee (46), or Wikidata (47).”
New and continuing developments at PROSITE (2012, methodology): “Users can also limit their results to only those proteins that are expressed in one of 56 adult tissues, using data from the Bgee resource (http://bgee.unil.ch/bgee/bgee), a database of gene expression and evolution (11).”