{"doi":"10.1371/journal.pcbi.1010174","title":"Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues","abstract":"<jats:p>The increasingly large amount of proteomics data in the public domain 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 contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively.</jats:p>\n                  <jats:p>In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. 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, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.</jats:p>","journal":"PLOS Computational Biology","year":2022,"id":678461,"datarank":0.4493598410330987,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.0,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.0,"corpus_percentile":58.5,"corpus_rank":5726,"citation_count":19,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":80042,"name":"David García-Seisdedos","orcid":null,"position":1,"is_corresponding":false},{"id":80044,"name":"Ananth Prakash","orcid":"0000-0001-5799-9618","position":2,"is_corresponding":false},{"id":79927,"name":"Deepti J Kundu","orcid":"0000-0003-2989-5971","position":3,"is_corresponding":false},{"id":182106,"name":"Andrew Collins","orcid":"0000-0003-0507-6912","position":4,"is_corresponding":false},{"id":265741,"name":"Nancy George","orcid":"0000-0003-4183-8865","position":5,"is_corresponding":false},{"id":1772659,"name":"Silvie Fexova","orcid":"0000-0003-3440-1876","position":6,"is_corresponding":false},{"id":7601,"name":"Pablo Moreno","orcid":"0000-0002-9856-1679","position":7,"is_corresponding":false},{"id":13898,"name":"Irene Papatheodorou","orcid":"0000-0001-7270-5470","position":8,"is_corresponding":false},{"id":74630,"name":"Andrew R. Jones","orcid":"0000-0001-6118-9327","position":9,"is_corresponding":false},{"id":17887,"name":"Juan Antonio Vizcaino","orcid":"0000-0002-3905-4335","position":10,"is_corresponding":false},{"id":80046,"name":"Shengbo Wang","orcid":"0000-0001-5034-6374","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues","abstract":"<jats:p>The increasingly large amount of proteomics data in the public domain 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 contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively.</jats:p>\n                  <jats:p>In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. 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, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.</jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35714157","pmcid":"PMC9246241","openalex_id":null,"authors":[],"funders":[{"funder_name":"Open Targets","grant_id":"OTAR-02-068","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BBSRC BB/T019670/1","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BBSRC BB/T019557/1","title":null},{"funder_name":"Wellcome Trust","grant_id":"208391/Z/17/Z","title":null},{"funder_name":"European Molecular Biology Laboratory","grant_id":"EMBL core funding","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/T019557/1","title":"GRAPPA - Global compRehensive Atlas of Peptide and Protein Abundance"},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/T019670/1","title":"GRAPPA - Global compRehensive Atlas of Peptide and Protein Abundance"},{"funder_name":"Wellcome Trust","grant_id":"208391","title":"The PRIDE database: A proteomics data hub in the life sciences"},{"funder_name":"Wellcome Trust","grant_id":"unidentified","title":"unidentified"},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":10,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1371/journal.pcbi.1010174","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pcbi.1010174","host_type":"publisher"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9246241","host_type":"repository"},{"url":"https://doaj.org/article/849f32e493854c30839c111727f66dc3","host_type":"repository"},{"url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010174&type=printable","host_type":"Unpaywall"},{"url":"https://europepmc.org/articles/PMC9246241","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9246241?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1101/2021.12.20.473413","host_type":""},{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/12/21/2021.12.20.473413.full.pdf","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/35714157","host_type":""},{"url":"http://dx.doi.org/10.1371/journal.pcbi.1010174","host_type":""}],"fields_of_study":["0301 basic medicine","03 medical and health sciences"],"mesh_terms":["Brain","Animals","Mice","Rats","Proteins","Proteomics"],"keywords":["Proteomics","Mice","QH301-705.5","Animals","Brain","Proteins","Biology (General)","Research Article","Rats"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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