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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\u2019s paradox. By utilizing public domain data, CoRegNet offers a powerful approach for identifying functionally related gene pairs, thereby revealing new biological insights.<\/jats:p>","DOI":"10.1093\/bib\/bbad380","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:19:55Z","timestamp":1697131195000},"source":"Crossref","is-referenced-by-count":4,"title":["CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model"],"prefix":"10.1093","volume":"25","author":[{"given":"Jiasheng","family":"Wang","sequence":"first","affiliation":[{"name":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA"},{"name":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA"},{"name":"Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , 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USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhandong","family":"Liu","sequence":"additional","affiliation":[{"name":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA"},{"name":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA"},{"name":"Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,12,18]]},"reference":[{"key":"2023121916214503700_ref1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids 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