{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:28:29Z","timestamp":1761514109190,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,29]],"date-time":"2017-11-29T00:00:00Z","timestamp":1511913600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-CA194391 and P50-CA070907-18","R01160736","P30-CA016672"],"award-info":[{"award-number":["R01-CA194391 and P50-CA070907-18","R01160736","P30-CA016672"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1463233"],"award-info":[{"award-number":["1463233"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Differential network analysis is an important way to understand network rewiring involved in disease progression and development. Building differential networks from multiple \u2018omics data provides insight into the holistic differences of the interactive system under different patient-specific groups. DINGO was developed to infer group-specific dependencies and build differential networks. However, DINGO and other existing tools are limited to analyze data arising from a single platform, and modeling each of the multiple \u2018omics data independently does not account for the hierarchical structure of the data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed the iDINGO R package to estimate group-specific dependencies and make inferences on the integrative differential networks, considering the biological hierarchy among the platforms. A Shiny application has also been developed to facilitate easier analysis and visualization of results, including integrative differential networks and hub gene identification across platforms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R package is available on CRAN (https:\/\/cran.r-project.org\/web\/packages\/iDINGO) and Shiny application at https:\/\/github.com\/MinJinHa\/iDINGO.<\/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\/btx750","type":"journal-article","created":{"date-parts":[[2017,11,28]],"date-time":"2017-11-28T20:15:11Z","timestamp":1511900111000},"page":"1243-1245","source":"Crossref","is-referenced-by-count":18,"title":["iDINGO\u2014integrative differential network analysis in genomics with <i>Shiny<\/i> application"],"prefix":"10.1093","volume":"34","author":[{"given":"Caleb A","family":"Class","sequence":"first","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Min Jin","family":"Ha","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Veerabhadran","family":"Baladandayuthapani","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Kim-Anh","family":"Do","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,11,29]]},"reference":[{"key":"2023012712573356200_btx750-B1","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1126\/science.1195618","article-title":"Rewiring of genetic networks in response to DNA damage","volume":"330","author":"Bandyopadhyay","year":"2010","journal-title":"Science"},{"key":"2023012712573356200_btx750-B2","doi-asserted-by":"crossref","DOI":"10.1038\/msb.2010.117","article-title":"Rewiring makes the difference","volume":"7","author":"Califano","year":"2011","journal-title":"Mol. 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