Expression Atlas update: gene and protein expression in multiple species

Moreno, Pablo; Fexová, Silvie; George, Nancy; Manning, Jonathan; Miao, Zhichao; Mohammed, Suhaib; Muñoz-Pomer, Alfonso; Füllgrabe, Anja; Bi, Yalan; Bush, Natassja G.; Iqbal, Haider; Kumbham, Upendra; Solovyev, A.G.; Zhao, Lingyun; Prakash, Ananth; García-Seisdedos, David; Kundu, Deepti Jaiswal; Wang, Shengbo; Walzer, Mathias; Clarke, Laura; Osumi-Sutherland, David; Tello-Ruiz, Marcela K.; Kumari, Sunita; Ware, Doreen; Eliasova, Jana; Arends, Mark J.; Nawijn, Martijn C.; Meyer, Kerstin B.; Burdett, Tony; Marioni, John C.; Teichmann, Sarah A.; Vizcaíno, Juan Antonio; Brāzma, Alvis; Papatheodorou, Irene

doi:10.1093/nar/gkab1030

Cited by 135 publications

(84 citation statements)

References 38 publications

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“…The Expression widget also contains hyperlinks to primary sources of annotated data, e.g. the MODs, and external sources of gene expression data, such as Gene Expression Omnibus ( Clough and Barrett 2016 https://www.ncbi.nlm.nih.gov/geo/ [accessed 2022 Jan 16] ); the Expression Atlas ( Papatheodorou et al 2020 , https://www.ebi.ac.uk/gxa/home [accessed 2022 Jan 16]), and the Single Cell Expression Atlas ( Moreno et al 2022 , https://www.ebi.ac.uk/gxa/sc/home [accessed 2022 Jan 16]). Expression data can also be downloaded in bulk for all organisms or for individual species on the Data Download page ( https://www.alliancegenome.org/downloads [accessed 2022 Jan 16]).…”

Section: Introduction: the Model Organism Databases The Goals And The...mentioning

confidence: 99%

Harmonizing model organism data in the Alliance of Genome Resources

Agapite¹,

Albou²,

Aleksander³

et al. 2022

Genetics

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The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

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Section: Introduction: the Model Organism Databases The Goals And The...mentioning

confidence: 99%

Harmonizing model organism data in the Alliance of Genome Resources

Agapite¹,

Albou²,

Aleksander³

et al. 2022

Genetics

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“…This is perceived as a more sustainable approach in the medium-long term than setting up new bioinformatics resources. One of them is Expression Atlas [13], a resource that has enabled over the years easy access to gene expression data across species, tissues, cells, experimental conditions and diseases. Only recently, protein expression information coming from reanalysed datasets has been integrated in the 'bulk' section of Expression Atlas.…”

Section: Introductionmentioning

confidence: 99%

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Wang

García-Seisdedos

Prakash

et al. 2021

Preprint

Self Cite

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The increasingly large amount of public proteomics data enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contains 23 individual datasets, which have a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We compared protein expression between the different organs, including the distribution of proteins across them. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples. Finally, it should be noted that protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

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“…The Plant Cistrome TF binding profiles collection (processed by the GEM in O’Malley et al, 2016 ) consisted of 568 peak sets for 387 TFs. We collected the benchmark compilation of 114 uniformly processed RNA-seq datasets from the EBI Expression Atlas ( Moreno et al, 2022 ; see Supplementary Table 1 ), 1 and five RNA-seq datasets on auxin treatments on arabidopsis seedlings/roots were taken from Freire-Rios et al (2020) .…”

Section: Methodsmentioning

confidence: 99%

CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

et al. 2022

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Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.

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Expression Atlas update: gene and protein expression in multiple species

Cited by 135 publications

References 38 publications

Harmonizing model organism data in the Alliance of Genome Resources

Harmonizing model organism data in the Alliance of Genome Resources

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

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