{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T18:57:30Z","timestamp":1775588250144,"version":"3.50.1"},"reference-count":131,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2016,4,14]],"date-time":"2016-04-14T00:00:00Z","timestamp":1460592000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004820","type":"journal-article","created":{"date-parts":[[2016,4,14]],"date-time":"2016-04-14T18:58:18Z","timestamp":1460660298000},"page":"e1004820","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Computational Reconstruction of NF\u03baB Pathway Interaction Mechanisms during Prostate Cancer"],"prefix":"10.1371","volume":"12","author":[{"given":"Daniela","family":"B\u00f6rnigen","sequence":"first","affiliation":[]},{"given":"Svitlana","family":"Tyekucheva","sequence":"additional","affiliation":[]},{"given":"Xiaodong","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Jennifer R.","family":"Rider","sequence":"additional","affiliation":[]},{"given":"Gwo-Shu","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Lorelei A.","family":"Mucci","sequence":"additional","affiliation":[]},{"given":"Christopher","family":"Sweeney","sequence":"additional","affiliation":[]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2016,4,14]]},"reference":[{"issue":"Suppl","key":"ref1","doi-asserted-by":"crossref","first-page":"S81","DOI":"10.1016\/S0092-8674(02)00703-1","article-title":"Missing pieces in the NF-kappaB puzzle","volume":"109","author":"S Ghosh","year":"2002","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/ni0302-221","article-title":"NF-kappaB at the crossroads of life and death","volume":"3","author":"M Karin","year":"2002","journal-title":"Nat Immunol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/jcb.10729","article-title":"NF-kappaB activation in human prostate cancer: important mediator or epiphenomenon?","volume":"91","author":"J Suh","year":"2004","journal-title":"J Cell Biochem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"a000141","DOI":"10.1101\/cshperspect.a000141","article-title":"NF-kappaB as a critical link between inflammation and cancer","volume":"1","author":"M Karin","year":"2009","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"489","DOI":"10.2353\/ajpath.2009.080727","article-title":"NF-kappaB regulates androgen receptor expression and prostate cancer growth","volume":"175","author":"L Zhang","year":"2009","journal-title":"Am J Pathol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"6717","DOI":"10.1038\/sj.onc.1209937","article-title":"Post-translational modifications regulating the activity and function of the nuclear factor kappa B pathway","volume":"25","author":"ND Perkins","year":"2006","journal-title":"Oncogene"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/nrc3204","article-title":"The diverse and complex roles of NF-kappaB subunits in cancer","volume":"12","author":"ND Perkins","year":"2012","journal-title":"Nat Rev Cancer"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"5501","DOI":"10.1158\/1078-0432.CCR-0571-03","article-title":"Nuclear factor-kappaB is constitutively activated in prostate cancer in vitro and is overexpressed in prostatic intraepithelial neoplasia and adenocarcinoma of the prostate","volume":"10","author":"C Sweeney","year":"2004","journal-title":"Clin Cancer Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1002\/pros.21141","article-title":"A water-soluble parthenolide analogue suppresses in vivo prostate cancer growth by targeting NFkappaB and generating reactive oxygen species","volume":"70","author":"R Shanmugam","year":"2010","journal-title":"Prostate"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1667\/RR1394.1","article-title":"Suppression of NF-kappaB activity by parthenolide induces X-ray sensitivity through inhibition of split-dose repair in TP53 null prostate cancer cells","volume":"171","author":"C Watson","year":"2009","journal-title":"Radiat Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1498","DOI":"10.1002\/pros.20482","article-title":"Restoring chemotherapy and hormone therapy sensitivity by parthenolide in a xenograft hormone refractory prostate cancer model","volume":"66","author":"R Shanmugam","year":"2006","journal-title":"Prostate"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2481","DOI":"10.1002\/ijc.25587","article-title":"A water soluble parthenolide analog suppresses in vivo tumor growth of two tobacco-associated cancers, lung and bladder cancer, by targeting NF-kappaB and generating reactive oxygen species","volume":"128","author":"R Shanmugam","year":"2011","journal-title":"Int J Cancer"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1158\/1055-9965.EPI-10-0994","article-title":"Genetic polymorphisms in inflammation pathway genes and prostate cancer risk","volume":"20","author":"EM Kwon","year":"2011","journal-title":"Cancer Epidemiol Biomarkers Prev"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1158\/1055-9965.EPI-11-0236","article-title":"Genetic variants in the LEPR, CRY1, RNASEL, IL4, and ARVCF genes are prognostic markers of prostate cancer-specific mortality","volume":"20","author":"DW Lin","year":"2011","journal-title":"Cancer Epidemiol Biomarkers Prev"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/1471-2407-7-64","article-title":"Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process","volume":"7","author":"UR Chandran","year":"2007","journal-title":"BMC Cancer"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.cell.2008.01.020","article-title":"Shared principles in NF-kappaB signaling","volume":"132","author":"MS Hayden","year":"2008","journal-title":"Cell"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/j.1600-065X.2011.01059.x","article-title":"Non-canonical NF-kappaB signaling activation and regulation: principles and perspectives","volume":"244","author":"B Razani","year":"2011","journal-title":"Immunol Rev"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.cytogfr.2011.11.002","article-title":"Regulation of TNF-induced NF-kappaB activation by different cytoplasmic ubiquitination events","volume":"22","author":"K Verhelst","year":"2011","journal-title":"Cytokine Growth Factor Rev"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2827","DOI":"10.2174\/1381612043383584","article-title":"The NF-kappaB pathway as a potential target for autoimmune disease therapy","volume":"10","author":"S Bacher","year":"2004","journal-title":"Curr Pharm Des"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1136\/amiajnl-2011-000178","article-title":"Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence","volume":"18","author":"JL Chen","year":"2011","journal-title":"J Am Med Inform Assoc"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.jbi.2010.03.009","article-title":"Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures","volume":"43","author":"J Chen","year":"2010","journal-title":"J Biomed Inform"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/msb4100180","article-title":"Network-based classification of breast cancer metastasis","volume":"3","author":"HY Chuang","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"202ra122","DOI":"10.1126\/scitranslmed.3006408","article-title":"A molecular signature predictive of indolent prostate cancer","volume":"5","author":"S Irshad","year":"2013","journal-title":"Sci Transl Med"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1001009","DOI":"10.1371\/journal.pcbi.1001009","article-title":"Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components","volume":"6","author":"CY Park","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1755-8794-3-8","article-title":"Molecular sampling of prostate cancer: a dilemma for predicting disease progression","volume":"3","author":"A Sboner","year":"2010","journal-title":"BMC Med Genomics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/jnci\/djn150","article-title":"Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer","volume":"100","author":"SR Setlur","year":"2008","journal-title":"J Natl Cancer Inst"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"D1007","DOI":"10.1093\/nar\/gkt1166","article-title":"Lynx: a database and knowledge extraction engine for integrative medicine","volume":"42","author":"D Sulakhe","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1056\/NEJM199802123380706","article-title":"Chemokines\u2014chemotactic cytokines that mediate inflammation","volume":"338","author":"AD Luster","year":"1998","journal-title":"N Engl J Med"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1083\/jcb.201102147","article-title":"The extracellular matrix: a dynamic niche in cancer progression","volume":"196","author":"P Lu","year":"2012","journal-title":"J Cell Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"6528","DOI":"10.1073\/pnas.85.17.6528","article-title":"Amphiregulin: a bifunctional growth-modulating glycoprotein produced by the phorbol 12-myristate 13-acetate-treated human breast adenocarcinoma cell line MCF-7","volume":"85","author":"M Shoyab","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2411","DOI":"10.1093\/emboj\/cdg231","article-title":"TACE cleavage of proamphiregulin regulates GPCR-induced proliferation and motility of cancer cells","volume":"22","author":"A Gschwind","year":"2003","journal-title":"EMBO J"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/S0002-9378(97)70213-8","article-title":"Circulating endothelial cell adhesion molecules as diagnostic markers for the early identification of pregnant women at risk for development of preeclampsia","volume":"177","author":"T Krauss","year":"1997","journal-title":"Am J Obstet Gynecol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"4637","DOI":"10.4049\/jimmunol.162.8.4637","article-title":"Complex conserved organization of the mammalian leukemia inhibitory factor gene: regulated expression of intracellular and extracellular cytokines","volume":"162","author":"BP Haines","year":"1999","journal-title":"J Immunol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1023\/A:1007075701551","article-title":"Toxoplasma gondii induces the secretion of monocyte chemotactic protein-1 in human fibroblasts, in vitro","volume":"209","author":"MP Brenier-Pinchart","year":"2000","journal-title":"Mol Cell Biochem"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1097\/00006676-200007000-00051","article-title":"Autocrine growth effect of IL-8 and GROalpha on a human pancreatic cancer cell line, Capan-1","volume":"21","author":"H Takamori","year":"2000","journal-title":"Pancreas"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"5846","DOI":"10.1074\/jbc.272.9.5846","article-title":"Molecular cloning of a novel human CC chemokine liver and activation-regulated chemokine (LARC) expressed in liver. Chemotactic activity for lymphocytes and gene localization on chromosome 2","volume":"272","author":"K Hieshima","year":"1997","journal-title":"J Biol Chem"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.psychres.2009.02.007","article-title":"CCL3 correlates with the number of mood disturbances and personality changes in patients with Alzheimer's disease","volume":"176","author":"AM Geppert","year":"2010","journal-title":"Psychiatry Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1074\/jbc.274.2.956","article-title":"Agonists and inverse agonists for the herpesvirus 8-encoded constitutively active seven-transmembrane oncogene product, ORF-74","volume":"274","author":"MM Rosenkilde","year":"1999","journal-title":"J Biol Chem"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"a000166","DOI":"10.1101\/cshperspect.a000166","article-title":"Ubiquitination and degradation of the inhibitors of NF-kappaB","volume":"2","author":"N Kanarek","year":"2010","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"6351","DOI":"10.1093\/emboj\/19.23.6351","article-title":"The anti-apoptotic activities of Rel and RelA required during B-cell maturation involve the regulation of Bcl-2 expression","volume":"19","author":"M Grossmann","year":"2000","journal-title":"EMBO J"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/cdd.2011.158","article-title":"BCL2A1: the underdog in the BCL2 family","volume":"19","author":"M Vogler","year":"2012","journal-title":"Cell Death Differ"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/nrc780","article-title":"NF-kappaB in cancer: from innocent bystander to major culprit","volume":"2","author":"M Karin","year":"2002","journal-title":"Nat Rev Cancer"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"38069","DOI":"10.1074\/jbc.M110.147207","article-title":"Classical NF-kappaB activation negatively regulates noncanonical NF-kappaB-dependent CXCL12 expression","volume":"285","author":"LA Madge","year":"2010","journal-title":"J Biol Chem"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1006\/bbrc.1997.6665","article-title":"Interleukin-18 activates NF-kappaB in murine T helper type 1 cells","volume":"234","author":"S Matsumoto","year":"1997","journal-title":"Biochem Biophys Res Commun"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1002\/ijc.23109","article-title":"EGFR induces expression of IRF-1 via STAT1 and STAT3 activation leading to growth arrest of human cancer cells","volume":"122","author":"P Andersen","year":"2008","journal-title":"Int J Cancer"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.cytogfr.2009.11.005","article-title":"Dangerous liaisons: STAT3 and NF-kappaB collaboration and crosstalk in cancer","volume":"21","author":"SI Grivennikov","year":"2010","journal-title":"Cytokine Growth Factor Rev"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"E1470","DOI":"10.1073\/pnas.1215938110","article-title":"TPL2 kinase is a suppressor of lung carcinogenesis","volume":"110","author":"K Gkirtzimanaki","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"e16205","DOI":"10.1371\/journal.pone.0016205","article-title":"TPL2\/COT\/MAP3K8 (TPL2) activation promotes androgen depletion-independent (ADI) prostate cancer growth","volume":"6","author":"JH Jeong","year":"2011","journal-title":"PLoS One"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"e28577","DOI":"10.1371\/journal.pone.0028577","article-title":"Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy","volume":"6","author":"RA Tamboli","year":"2011","journal-title":"PLoS One"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"6721","DOI":"10.1073\/pnas.93.13.6721","article-title":"The tumor necrosis factor-inducible zinc finger protein A20 interacts with TRAF1\/TRAF2 and inhibits NF-kappaB activation","volume":"93","author":"HY Song","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.cell.2012.04.042","article-title":"A CXCL1 paracrine network links cancer chemoresistance and metastasis","volume":"150","author":"S Acharyya","year":"2012","journal-title":"Cell"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/leu.2011.101","article-title":"Tumor suppressor TNFAIP3 (A20) is frequently deleted in Sezary syndrome","volume":"25","author":"FC Braun","year":"2011","journal-title":"Leukemia"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"18949","DOI":"10.1074\/jbc.M111.232637","article-title":"KAI1 gene is engaged in NDRG1 gene-mediated metastasis suppression through the ATF3-NFkappaB complex in human prostate cancer","volume":"286","author":"W Liu","year":"2011","journal-title":"J Biol Chem"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"29795","DOI":"10.1074\/jbc.M802515200","article-title":"KLF6 induces apoptosis in prostate cancer cells through up-regulation of ATF3","volume":"283","author":"X Huang","year":"2008","journal-title":"J Biol Chem"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1038\/sj.emboj.7601539","article-title":"Critical role for NF-kappaB-induced JunB in VEGF regulation and tumor angiogenesis","volume":"26","author":"D Schmidt","year":"2007","journal-title":"EMBO J"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"5197","DOI":"10.1242\/jcs.01483","article-title":"Linking JNK signaling to NF-kappaB: a key to survival","volume":"117","author":"S Papa","year":"2004","journal-title":"J Cell Sci"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/nature12688","article-title":"A melanocyte lineage program confers resistance to MAP kinase pathway inhibition","volume":"504","author":"CM Johannessen","year":"2013","journal-title":"Nature"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/ncomms1272","article-title":"The nuclear orphan receptor Nr4a2 induces Foxp3 and regulates differentiation of CD4+ T cells","volume":"2","author":"T Sekiya","year":"2011","journal-title":"Nat Commun"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1016\/j.cellsig.2009.07.015","article-title":"Regulation of the inducible nuclear dual-specificity phosphatase DUSP5 by ERK MAPK","volume":"21","author":"A Kucharska","year":"2009","journal-title":"Cell Signal"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1093\/emboj\/16.6.1413","article-title":"I kappa B epsilon, a novel member of the I kappa B family, controls RelA and cRel NF-kappa B activity","volume":"16","author":"ST Whiteside","year":"1997","journal-title":"EMBO J"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/0-306-48158-8_10","article-title":"The Re1\/NF-kappa B\/I kappa B signal transduction pathway and cancer","volume":"115","author":"TD Gilmore","year":"2003","journal-title":"Cancer Treat Res"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"e21726","DOI":"10.1371\/journal.pone.0021726","article-title":"NFkappaB1 and NFkappaBIA polymorphisms are associated with increased risk for sporadic colorectal cancer in a southern Chinese population","volume":"6","author":"S Song","year":"2011","journal-title":"PLoS One"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"3554","DOI":"10.1038\/sj.onc.1206418","article-title":"A novel mechanism of tumor suppression by destabilizing AU-rich growth factor mRNA","volume":"22","author":"G Stoecklin","year":"2003","journal-title":"Oncogene"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"29571","DOI":"10.1074\/jbc.M109.031237","article-title":"Tristetraprolin impairs NF-kappaB\/p65 nuclear translocation","volume":"284","author":"YM Schichl","year":"2009","journal-title":"J Biol Chem"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"4717","DOI":"10.4049\/jimmunol.0902444","article-title":"CXC chemokine ligand 2 induced by receptor activator of NF-kappa B ligand enhances osteoclastogenesis","volume":"184","author":"J Ha","year":"2010","journal-title":"J Immunol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"16163","DOI":"10.1074\/jbc.M412713200","article-title":"MCP-1 is induced by receptor activator of nuclear factor-{kappa}B ligand, promotes human osteoclast fusion, and rescues granulocyte macrophage colony-stimulating factor suppression of osteoclast formation","volume":"280","author":"MS Kim","year":"2005","journal-title":"J Biol Chem"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1186\/1471-2407-11-285","article-title":"Survival advantages conferred to colon cancer cells by E-selectin-induced activation of the PI3K-NFkappaB survival axis downstream of Death receptor-3","volume":"11","author":"N Porquet","year":"2011","journal-title":"BMC Cancer"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1073\/pnas.87.5.1673","article-title":"Endothelial leukocyte adhesion molecule 1: direct expression cloning and functional interactions","volume":"87","author":"C Hession","year":"1990","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1084\/jem.20070183","article-title":"Enhanced TLR-mediated NF-IL6 dependent gene expression by Trib1 deficiency","volume":"204","author":"M Yamamoto","year":"2007","journal-title":"J Exp Med"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1101\/gr.082214.108","article-title":"Exploring the human genome with functional maps","volume":"19","author":"C Huttenhower","year":"2009","journal-title":"Genome Res"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1093\/bioinformatics\/btn237","article-title":"The Sleipnir library for computational functional genomics","volume":"24","author":"C Huttenhower","year":"2008","journal-title":"Bioinformatics"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"4470","DOI":"10.4049\/jimmunol.165.8.4470","article-title":"Regulated production and molecular diversity of human liver and activation-regulated chemokine\/macrophage inflammatory protein-3 alpha from normal and transformed cells","volume":"165","author":"E Schutyser","year":"2000","journal-title":"J Immunol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"D1077","DOI":"10.1093\/nar\/gkr913","article-title":"Gene Expression Atlas update\u2014a value-added database of microarray and sequencing-based functional genomics experiments","volume":"40","author":"M Kapushesky","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.ccr.2005.10.001","article-title":"Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression","volume":"8","author":"S Varambally","year":"2005","journal-title":"Cancer Cell"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","article-title":"Hierarchical multi-label prediction of gene function","volume":"22","author":"Z Barutcuoglu","year":"2006","journal-title":"Bioinformatics"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/30918","article-title":"Collective dynamics of 'small-world' networks","volume":"393","author":"DJ Watts","year":"1998","journal-title":"Nature"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell's functional organization","volume":"5","author":"AL Barabasi","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/ncb1086","article-title":"A physical and functional map of the human TNF-alpha\/NF-kappa B signal transduction pathway","volume":"6","author":"T Bouwmeester","year":"2004","journal-title":"Nat Cell Biol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"7966","DOI":"10.1128\/MCB.25.18.7966-7975.2005","article-title":"NF-kappaB RelA phosphorylation regulates RelA acetylation","volume":"25","author":"LF Chen","year":"2005","journal-title":"Mol Cell Biol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"7065","DOI":"10.1128\/MCB.21.20.7065-7077.2001","article-title":"The p65 (RelA) subunit of NF-kappaB interacts with the histone deacetylase (HDAC) corepressors HDAC1 and HDAC2 to negatively regulate gene expression","volume":"21","author":"BP Ashburner","year":"2001","journal-title":"Mol Cell Biol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1093\/carcin\/bgh130","article-title":"Phosphorylation of FADD is critical for sensitivity to anticancer drug-induced apoptosis","volume":"25","author":"K Shimada","year":"2004","journal-title":"Carcinogenesis"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/s00011-013-0590-7","article-title":"NF-kappaB RNAi decreases the Bax\/Bcl-2 ratio and inhibits TNF-alpha-induced apoptosis in human alveolar epithelial cells","volume":"62","author":"L Li","year":"2013","journal-title":"Inflamm Res"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1016\/j.bbagen.2013.03.006","article-title":"Transcriptional and post-translational regulation of Bim is essential for TGF-beta and TNF-alpha-induced apoptosis of gastric cancer cell","volume":"1830","author":"HT Ha Thi","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/nm.3085","article-title":"Phosphorylation of FOXP3 controls regulatory T cell function and is inhibited by TNF-alpha in rheumatoid arthritis","volume":"19","author":"H Nie","year":"2013","journal-title":"Nat Med"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"D199","DOI":"10.1093\/nar\/gkt1076","article-title":"Data, information, knowledge and principle: back to metabolism in KEGG","volume":"42","author":"M Kanehisa","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"D472","DOI":"10.1093\/nar\/gkt1102","article-title":"The Reactome pathway knowledgebase","volume":"42","author":"D Croft","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","author":"CF Schaefer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1056\/NEJMra021562","article-title":"Prostate cancer","volume":"349","author":"WG Nelson","year":"2003","journal-title":"N Engl J Med"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/35094009","article-title":"The development of androgen-independent prostate cancer","volume":"1","author":"BJ Feldman","year":"2001","journal-title":"Nat Rev Cancer"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/sj.pcan.4500776","article-title":"The emerging role of the PI3-K-Akt pathway in prostate cancer progression","volume":"8","author":"L Li","year":"2005","journal-title":"Prostate Cancer Prostatic Dis"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1158\/1078-0432.CCR-06-0067","article-title":"Mechanisms underlying the development of androgen-independent prostate cancer","volume":"12","author":"KJ Pienta","year":"2006","journal-title":"Clin Cancer Res"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"6083","DOI":"10.1093\/nar\/gki892","article-title":"Expansion of the BioCyc collection of pathway\/genome databases to 160 genomes","volume":"33","author":"PD Karp","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"W406","DOI":"10.1093\/nar\/gkr200","article-title":"The University of Minnesota Pathway Prediction System: multi-level prediction and visualization","volume":"39","author":"J Gao","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1093\/bioinformatics\/18.5.715","article-title":"Evaluation of computational metabolic-pathway predictions for Helicobacter pylori","volume":"18","author":"SM Paley","year":"2002","journal-title":"Bioinformatics"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/ng.620","article-title":"Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes","volume":"42","author":"G Nikoloski","year":"2010","journal-title":"Nat Genet"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1002\/ajmg.a.33557","article-title":"Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis","volume":"152A","author":"HC Mefford","year":"2010","journal-title":"Am J Med Genet A"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1002\/ajmg.a.33618","article-title":"Characterization of the chromosome 1q41q42.12 region, and the candidate gene DISP1, in patients with CDH","volume":"152A","author":"S Kantarci","year":"2010","journal-title":"Am J Med Genet A"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"3482","DOI":"10.1093\/hmg\/ddq264","article-title":"Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease","volume":"19","author":"K Fransen","year":"2010","journal-title":"Hum Mol Genet"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/bib\/bbq007","article-title":"A guide to web tools to prioritize candidate genes","volume":"12","author":"LC Tranchevent","year":"2011","journal-title":"Brief Bioinform"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"3081","DOI":"10.1093\/bioinformatics\/bts581","article-title":"An unbiased evaluation of gene prioritization tools","volume":"28","author":"D B\u00f6rnigen","year":"2012","journal-title":"Bioinformatics"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrg3253","article-title":"Computational tools for prioritizing candidate genes: boosting disease gene discovery","volume":"13","author":"Y Moreau","year":"2012","journal-title":"Nat Rev Genet"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1093\/nar\/gkt661","article-title":"Concordance of gene expression in human protein complexes reveals tissue specificity and pathology","volume":"41","author":"D B\u00f6rnigen","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"20870","DOI":"10.1073\/pnas.0810772105","article-title":"A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes","volume":"105","author":"K Lage","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"340758","DOI":"10.1155\/2014\/340758","article-title":"Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease","volume":"2014","author":"W Kong","year":"2014","journal-title":"Comput Math Methods Med"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1038\/15531","article-title":"Leukaemia disease genes: large-scale cloning and pathway predictions","volume":"23","author":"J Li","year":"1999","journal-title":"Nat Genet"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1093\/bioinformatics\/btt290","article-title":"Differential network analysis for the identification of condition-specific pathway activity and regulation","volume":"29","author":"G Gambardella","year":"2013","journal-title":"Bioinformatics"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/2043-9113-3-19","article-title":"Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks","volume":"3","author":"MF Islam","year":"2013","journal-title":"J Clin Bioinforma"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1016\/j.cell.2013.10.031","article-title":"Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism","volume":"155","author":"NN Parikshak","year":"2013","journal-title":"Cell"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"R55","DOI":"10.1186\/gb-2009-10-5-r55","article-title":"Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease","volume":"10","author":"R Dobrin","year":"2009","journal-title":"Genome Biol"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1517\/14728222.11.2.111","article-title":"NF-kappa B as a therapeutic target in autoimmune disease","volume":"11","author":"B O'Sullivan","year":"2007","journal-title":"Expert Opin Ther Targets"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"18754","DOI":"10.1073\/pnas.0704908104","article-title":"Selective inhibition of NF-kappaB activation prevents dopaminergic neuronal loss in a mouse model of Parkinson's disease","volume":"104","author":"A Ghosh","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/1476-4598-12-86","article-title":"The complexity of NF-kappaB signaling in inflammation and cancer","volume":"12","author":"B Hoesel","year":"2013","journal-title":"Mol Cancer"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1038\/nm.2890","article-title":"Treatment-induced damage to the tumor microenvironment promotes prostate cancer therapy resistance through WNT16B","volume":"18","author":"Y Sun","year":"2012","journal-title":"Nat Med"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.ccr.2013.03.022","article-title":"Mutant p53 prolongs NF-kappaB activation and promotes chronic inflammation and inflammation-associated colorectal cancer","volume":"23","author":"T Cooks","year":"2013","journal-title":"Cancer Cell"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"17117","DOI":"10.1073\/pnas.1114420108","article-title":"Tumor suppressor protein (p)53, is a regulator of NF-kappaB repression by the glucocorticoid receptor","volume":"108","author":"SH Murphy","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"3485","DOI":"10.1128\/MCB.19.5.3485","article-title":"Transcriptional cross talk between NF-kappaB and p53","volume":"19","author":"GA Webster","year":"1999","journal-title":"Mol Cell Biol"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gkq1184","article-title":"NCBI GEO: archive for functional genomics data sets\u201410 years on","volume":"39","author":"T Barrett","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"e791","DOI":"10.7717\/peerj.791","article-title":"A reproducible approach to high-throughput biological data acquisition and integration","volume":"3","author":"D B\u00f6rnigen","year":"2015","journal-title":"PeerJ"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"RA Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-11-5","article-title":"The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services","volume":"11","author":"MP van Iersel","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"D816","DOI":"10.1093\/nar\/gks1158","article-title":"The BioGRID interaction database: 2013 update","volume":"41","author":"A Chatr-Aryamontri","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"D452","DOI":"10.1093\/nar\/gkh052","article-title":"IntAct: an open source molecular interaction database","volume":"32","author":"H Hermjakob","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"STRING v9.1: protein-protein interaction networks, with increased coverage and integration","volume":"41","author":"A Franceschini","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"D227","DOI":"10.1093\/nar\/gkj063","article-title":"The PROSITE database","volume":"34","author":"N Hulo","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref126","doi-asserted-by":"crossref","first-page":"D730","DOI":"10.1093\/nar\/gkq1229","article-title":"DOMINE: a comprehensive collection of known and predicted domain-domain interactions","volume":"39","author":"S Yellaboina","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref127","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"V Matys","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref128","doi-asserted-by":"crossref","first-page":"D107","DOI":"10.1093\/nar\/gkm967","article-title":"ORegAnno: an open-access community-driven resource for regulatory annotation","volume":"36","author":"OL Griffith","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref129","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":"EG Cerami","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref130","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","article-title":"Human Protein Reference Database\u20142009 update","volume":"37","author":"TS Keshava Prasad","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref131","doi-asserted-by":"crossref","first-page":"6853","DOI":"10.1038\/sj.onc.1203239","article-title":"Activators and target genes of Rel\/NF-kappaB transcription factors","volume":"18","author":"HL Pahl","year":"1999","journal-title":"Oncogene"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004820","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,17]],"date-time":"2023-08-17T17:07:58Z","timestamp":1692292078000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004820"}},"subtitle":[],"editor":[{"given":"Teresa M.","family":"Przytycka","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,4,14]]},"references-count":131,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2016,4,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004820","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,14]]}}}