{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T22:25:04Z","timestamp":1785536704087,"version":"3.56.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T00:00:00Z","timestamp":1674432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Sciences Program\u2019 at HSE University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential expression analysis, differential co-expression one aims to detect pairs or clusters whose mutual expression changes between two conditions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed Differential Co-expression Network Analysis (DCoNA)\u2014an open-source statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing DCoNA with the state-of-the-art analog, we showed that DCoNA is a faster, more accurate and less memory-consuming tool. We applied DCoNA to prostate mRNA\/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) and compared predicted regulatory interactions of miRNA isoforms (isomiRs) and their target mRNAs between normal and cancer samples. As a result, almost all highly expressed isomiRs lost negative correlation with their targets in prostate cancer samples compared to ones without the pathology. One exception to this trend was the canonical isomiR of hsa-miR-93-5p acquiring cancer-specific targets. Further analysis showed that cancer aggressiveness simultaneously increased with the expression level of this isomiR in both TCGA primary tumor samples and 153 blood plasma samples of P. Hertsen Moscow Oncology Research Institute patients\u2019 cohort analyzed by miRNA microarrays.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code and documentation of DCoNA are available at https:\/\/github.com\/zhiyanov\/DCoNA.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad051","type":"journal-article","created":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T09:52:18Z","timestamp":1674467538000},"source":"Crossref","is-referenced-by-count":9,"title":["Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2866-9692","authenticated-orcid":false,"given":"Anton","family":"Zhiyanov","sequence":"first","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University , Moscow 101000, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3524-8586","authenticated-orcid":false,"given":"Narek","family":"Engibaryan","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University , Moscow 101000, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8830-4679","authenticated-orcid":false,"given":"Stepan","family":"Nersisyan","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia , Yerevan 0014, Armenia"},{"name":"Armenian Bioinformatics Institute (ABI) , Yerevan, Armenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxim","family":"Shkurnikov","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University , Moscow 101000, Russia"},{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow 117997, Russia"},{"name":"P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research , Moscow 125284, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Tonevitsky","sequence":"additional","affiliation":[{"name":"Faculty of Biology and Biotechnology, HSE University , Moscow 101000, Russia"},{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow 117997, Russia"},{"name":"Art Photonics GmbH , Berlin 12489, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,1,23]]},"reference":[{"key":"2023022409554604100_","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. 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