{"doi":"10.1093/bib/bbad380","title":"CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model","abstract":"Millions of RNA sequencing samples have been deposited into public databases, providing a rich resource for biological research. These datasets encompass tens of thousands of experiments and offer comprehensive insights into human cellular regulation. However, a major challenge is how to integrate these experiments that acquired at different conditions. We propose a new statistical tool based on beta-binomial distributions that can construct robust gene co-regulation network (CoRegNet) across tens of thousands of experiments. Our analysis of over 12 000 experiments involving human tissues and cells shows that CoRegNet significantly outperforms existing gene co-expression-based methods. Although the majority of the genes are linearly co-regulated, we did discover an interesting set of genes that are non-linearly co-regulated; half of the time they change in the same direction and the other half they change in the opposite direction. Additionally, we identified a set of gene pairs that follows the Simpson's paradox. By utilizing public domain data, CoRegNet offers a powerful approach for identifying functionally related gene pairs, thereby revealing new biological insights.","journal":"Briefings in Bioinformatics","year":2023,"id":382883,"datarank":0.21972765623750268,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.01178350206951907,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.01178350206951907,"corpus_percentile":37.27082849849153,"corpus_rank":8108,"citation_count":3,"citer_count":3,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7411,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":110454,"name":"Ying‐Wooi Wan","orcid":"0000-0002-4354-7482","position":1,"is_corresponding":false},{"id":234498,"name":"Rami Al‐Ouran","orcid":null,"position":2,"is_corresponding":false},{"id":1149767,"name":"Meichen Huang","orcid":null,"position":3,"is_corresponding":false},{"id":110460,"name":"Zhandong Liu","orcid":"0000-0002-7608-0831","position":4,"is_corresponding":false},{"id":1149360,"name":"Jiasheng Wang","orcid":"0000-0001-8477-7092","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-19T01:17:20.969491Z","pmid":"38113079","pmcid":"PMC10729864","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}