{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:52:09Z","timestamp":1761663129883,"version":"3.37.3"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":4144,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"name":"National Institute of Health","award":["GM79383","GM67168"],"award-info":[{"award-number":["GM79383","GM67168"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["30870474"],"award-info":[{"award-number":["30870474"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding the mechanism of complex human diseases is a major scientific challenge. Towards this end, we developed a web-based network tool named iBIG (stands for integrative BIoloGy), which incorporates a variety of information on gene interaction and regulation. The generated network can be annotated with various types of information and visualized directly online. In addition to the gene networks based on physical and pathway interactions, networks at a functional level can also be constructed. Furthermore, a supplementary R package is provided to process microarray data and generate a list of important genes to be used as input for iBIG. To demonstrate its usefulness, we collected 54 microarrays on common human diseases including cancer, neurological disorders, infectious diseases and other common diseases. We processed the microarray data with our R package and constructed a network of functional modules perturbed in common human diseases. Networks at the functional level in combination with gene networks may provide new insight into the mechanism of human diseases. iBIG is freely available at http:\/\/lei.big.ac.cn\/ibig.<\/jats:p>","DOI":"10.1016\/j.gpb.2012.08.007","type":"journal-article","created":{"date-parts":[[2013,1,4]],"date-time":"2013-01-04T21:17:21Z","timestamp":1357334241000},"page":"166-171","source":"Crossref","is-referenced-by-count":5,"title":["iBIG: An Integrative Network Tool for Supporting Human Disease Mechanism Studies"],"prefix":"10.1093","volume":"11","author":[{"given":"Jiya","family":"Sun","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"}]},{"given":"Yuyun","family":"Pan","sequence":"additional","affiliation":[{"name":"Graduate University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"given":"Xuemei","family":"Feng","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"}]},{"given":"Huijuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"given":"Yong","family":"Duan","sequence":"additional","affiliation":[{"name":"UC Davis Genome Center and Department of Biomedical Engineering , Davis, CA 95616 , USA"}]},{"given":"Hongxing","family":"Lei","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"UC Davis Genome Center and Department of Biomedical Engineering , Davis, CA 95616 , USA"}]}],"member":"286","published-online":{"date-parts":[[2013,1,4]]},"reference":[{"key":"2024051008325443700_b0005","doi-asserted-by":"crossref","first-page":"2952","DOI":"10.1093\/bioinformatics\/btl491","article-title":"BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network","volume":"22","author":"Chen","year":"2006","journal-title":"Bioinformatics"},{"key":"2024051008325443700_b0010","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2024051008325443700_b0015","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-11-91","article-title":"BisoGenet: a new tool for gene network building, visualization and analysis","volume":"11","author":"Martin","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2024051008325443700_b0020","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1093\/bioinformatics\/btn501","article-title":"Integrating and annotating the interactome using the MiMI plugin for cytoscape","volume":"25","author":"Gao","year":"2009","journal-title":"Bioinformatics"},{"key":"2024051008325443700_b0025","doi-asserted-by":"crossref","first-page":"2495","DOI":"10.1093\/bioinformatics\/btm373","article-title":"APID2NET: unified interactome graphic analyzer","volume":"23","author":"Hernandez-Toro","year":"2007","journal-title":"Bioinformatics"},{"key":"2024051008325443700_b0030","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0035","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1186\/1471-2105-11-393","article-title":"Compartmentalization of the Edinburgh Human Metabolic Network","volume":"11","author":"Hao","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2024051008325443700_b0040","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/nar\/gkn892","article-title":"Human protein reference database","volume":"37","author":"Keshava Prasad","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0045","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1093\/nar\/30.1.303","article-title":"DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions","volume":"30","author":"Xenarios","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0050","doi-asserted-by":"crossref","first-page":"D532","DOI":"10.1093\/nar\/gkp983","article-title":"MINT, the molecular interaction database: 2009 update","volume":"38","author":"Ceol","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0055","doi-asserted-by":"crossref","first-page":"D525","DOI":"10.1093\/nar\/gkp878","article-title":"The IntAct molecular interaction database in 2010","volume":"38","author":"Aranda","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0060","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1093\/bioinformatics\/16.5.465","article-title":"BIND \u2013 a data specification for storing and describing biomolecular interactions, molecular complexes and pathways","volume":"16","author":"Bader","year":"2000","journal-title":"Bioinformatics"},{"key":"2024051008325443700_b0065","doi-asserted-by":"crossref","first-page":"e120","DOI":"10.1093\/nar\/gkq149","article-title":"Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data","volume":"38","author":"Essaghir","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0070","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1261\/rna.2239606","article-title":"TarBase: a comprehensive database of experimentally supported animal microRNA targets","volume":"12","author":"Sethupathy","year":"2006","journal-title":"RNA"},{"key":"2024051008325443700_b0075","doi-asserted-by":"crossref","first-page":"D105","DOI":"10.1093\/nar\/gkn851","article-title":"MiRecords: an integrated resource for microRNA-target interactions","volume":"37","author":"Xiao","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0080","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1471-2164-9-172","article-title":"How many human genes can be defined as housekeeping with current expression data?","volume":"9","author":"Zhu","year":"2008","journal-title":"BMC Genomics"},{"key":"2024051008325443700_b0085","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1186\/1471-2164-10-269","article-title":"Definition, conservation and epigenetics of housekeeping and tissue-enriched genes","volume":"10","author":"She","year":"2009","journal-title":"BMC Genomics"},{"key":"2024051008325443700_b0090","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1471-2164-7-31","article-title":"Further understanding human disease genes by comparing with housekeeping genes and other genes","volume":"7","author":"Tu","year":"2006","journal-title":"BMC Genomics"},{"key":"2024051008325443700_b0095","doi-asserted-by":"crossref","first-page":"389","DOI":"10.3233\/JAD-2011-111313","article-title":"Down-regulation of energy metabolism in Alzheimer\u2019s disease is a protective response of neurons to the microenvironment","volume":"28","author":"Sun","year":"2012","journal-title":"J Alzheimers Dis"},{"key":"2024051008325443700_b0100","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1080\/00031305.1948.10483405","article-title":"Questions and answers #14","volume":"2","author":"Fisher","year":"1948","journal-title":"Am Stat"},{"key":"2024051008325443700_b0105","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2024051008325443700_b0110","doi-asserted-by":"crossref","first-page":"W352","DOI":"10.1093\/nar\/gki431","article-title":"VisANT: data-integrating visual framework for biological networks and modules","volume":"33","author":"Hu","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024051008325443700_b0115","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1093\/bioinformatics\/btq430","article-title":"Cytoscape web: an interactive web-based network browser","volume":"26","author":"Lopes","year":"2010","journal-title":"Bioinformatics"},{"key":"2024051008325443700_b0120","doi-asserted-by":"crossref","first-page":"e17715","DOI":"10.1371\/journal.pone.0017715","article-title":"A20 modulates lipid metabolism and energy production to promote liver regeneration","volume":"6","author":"Damrauer","year":"2011","journal-title":"PLoS One"},{"key":"2024051008325443700_b0125","doi-asserted-by":"crossref","first-page":"a004259","DOI":"10.1101\/cshperspect.a004259","article-title":"Calcium signaling in neuronal development","volume":"3","author":"Rosenberg","year":"2011","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2024051008325443700_b0130","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.2337\/diabetes.54.5.1264","article-title":"Insulin signaling in the central nervous system: a critical role in metabolic homeostasis and disease from C. elegans to humans","volume":"54","author":"Porte","year":"2005","journal-title":"Diabetes"},{"key":"2024051008325443700_b0135","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.lab.2005.10.005","article-title":"The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool","volume":"147","author":"Liew","year":"2006","journal-title":"J Lab Clin Med"},{"key":"2024051008325443700_b0140","first-page":"71","article-title":"Interaction between the coagulation and complement system","volume":"632","author":"Amara","year":"2008","journal-title":"Adv Exp Med Biol"},{"key":"2024051008325443700_b0145","doi-asserted-by":"crossref","first-page":"E131","DOI":"10.1038\/ncb0502-e131","article-title":"AP-1 as a regulator of cell life and death","volume":"4","author":"Shaulian","year":"2002","journal-title":"Nat Cell Biol"},{"key":"2024051008325443700_b0150","doi-asserted-by":"crossref","first-page":"10290","DOI":"10.1073\/pnas.0904227106","article-title":"Integrin beta1-focal adhesion kinase signaling directs the proliferation of metastatic cancer cells disseminated in the lungs","volume":"106","author":"Shibue","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024051008325443700_b0155","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1016\/j.ceb.2007.04.021","article-title":"Signaling on the endocytic pathway","volume":"19","author":"von Zastrow","year":"2007","journal-title":"Curr Opin Cell Biol"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022912001131?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022912001131?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/11\/3\/166\/57484703\/gpb_11_3_166.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/11\/3\/166\/57484703\/gpb_11_3_166.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T08:38:22Z","timestamp":1715330302000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/11\/3\/166\/7221938"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,4]]},"references-count":31,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2013,6,1]]}},"URL":"https:\/\/doi.org\/10.1016\/j.gpb.2012.08.007","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"type":"print","value":"1672-0229"},{"type":"electronic","value":"2210-3244"}],"subject":[],"published-other":{"date-parts":[[2013,6]]},"published":{"date-parts":[[2013,1,4]]}}}