{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T04:20:20Z","timestamp":1772770820856,"version":"3.50.1"},"reference-count":85,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,7]],"date-time":"2014-11-07T00:00:00Z","timestamp":1415318400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0112193","type":"journal-article","created":{"date-parts":[[2014,11,7]],"date-time":"2014-11-07T13:56:54Z","timestamp":1415368614000},"page":"e112193","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":56,"title":["Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis"],"prefix":"10.1371","volume":"9","author":[{"given":"Mohamed Diwan M.","family":"AbdulHameed","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregory J.","family":"Tawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamal","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danielle L.","family":"Ippolito","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John A.","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan D.","family":"Stallings","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Wallqvist","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2014,11,7]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1053\/j.gastro.2008.03.002","article-title":"Cellular and molecular mechanisms of liver injury","volume":"134","author":"H Malhi","year":"2008","journal-title":"Gastroenterology"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1515\/cclm-2011-0850","article-title":"Serum biomarkers for the non-invasive diagnosis of liver fibrosis: the importance of being validated","volume":"50","author":"G Sebastiani","year":"2012","journal-title":"Clin Chem Lab Med"},{"key":"ref3","first-page":"361","article-title":"Molecular pathogenesis of liver fibrosis","volume":"120","author":"DA Brenner","year":"2009","journal-title":"Trans Am Clin Climatol Assoc"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1172\/JCI24282","article-title":"Liver fibrosis","volume":"115","author":"R Bataller","year":"2005","journal-title":"J Clin Invest"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-230X-11-91","article-title":"Non-invasive markers for hepatic fibrosis","volume":"11","author":"A Baranova","year":"2011","journal-title":"BMC Gastroenterology"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"109","DOI":"10.3181\/0707-MR-190","article-title":"Mechanisms of fibrogenesis","volume":"233","author":"T Kisseleva","year":"2008","journal-title":"Exp Biol Med (Maywood)"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1002\/hep.26763","article-title":"Poly (ADP-ribose) polymerase-1 is a key mediator of liver inflammation and fibrosis","volume":"59","author":"P Mukhopadhyay","year":"2014","journal-title":"Hepatology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e73591","DOI":"10.1371\/journal.pone.0073591","article-title":"Aldose reductase is involved in the development of murine diet-induced nonalcoholic steatohepatitis","volume":"8","author":"L Qiu","year":"2013","journal-title":"PLOS ONE"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1111\/j.1440-1746.2010.06612.x","article-title":"Biomarkers of liver fibrosis","volume":"26","author":"LA Adams","year":"2011","journal-title":"J Gastroenterol Hepatol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1523\/JNEUROSCI.4098-07.2008","article-title":"A systems level analysis of transcriptional changes in Alzheimer&apos;s disease and normal aging","volume":"28","author":"JA Miller","year":"2008","journal-title":"J Neurosci"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"S225","DOI":"10.1093\/toxsci\/kfq373","article-title":"The evolution of bioinformatics in toxicology: advancing toxicogenomics","volume":"120","author":"CA Afshari","year":"2011","journal-title":"Toxicol Sci"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1752-0509-4-74","article-title":"Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression","volume":"4","author":"Z Shi","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1002\/hep.21921","article-title":"Antiangiogenic treatment with sunitinib ameliorates inflammatory infiltrate, fibrosis, and portal pressure in cirrhotic rats","volume":"46","author":"S Tugues","year":"2007","journal-title":"Hepatology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1089\/neu.2012.2631","article-title":"Systems biology approaches for discovering biomarkers for traumatic brain injury","volume":"30","author":"JD Feala","year":"2013","journal-title":"J Neurotrauma"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e107230","DOI":"10.1371\/journal.pone.0107230","article-title":"Characterization of chemically induced liver injuries using gene co-expression modules","volume":"9","author":"GJ Tawa","year":"2014","journal-title":"PLOS ONE"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkr988","article-title":"KEGG for integration and interpretation of large-scale molecular data sets","volume":"40","author":"M Kanehisa","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"D619","DOI":"10.1093\/nar\/gkn863","article-title":"Reactome knowledgebase of human biological pathways and processes","volume":"37","author":"L Matthews","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"D492","DOI":"10.1093\/nar\/gkp858","article-title":"The NCBI BioSystems database","volume":"38","author":"LY Geer","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1021\/ci4005354","article-title":"Pathway analysis for drug repositioning based on public database mining","volume":"54","author":"Y Pan","year":"2014","journal-title":"J Chem Inf Model"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"W Huang da","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1289\/ehp.1104282","article-title":"Inflammatory pathway genes belong to major targets of persistent organic pollutants in adipose cells","volume":"120","author":"MJ Kim","year":"2012","journal-title":"Environ Health Perspect"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"3108","DOI":"10.1158\/0008-5472.CAN-07-5644","article-title":"Subtypes of breast cancer show preferential site of relapse","volume":"68","author":"M Smid","year":"2008","journal-title":"Cancer Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/1471-2164-9-288","article-title":"Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants","volume":"9","author":"L Huang","year":"2008","journal-title":"BMC Genomics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1136\/gutjnl-2011-301146","article-title":"Transcriptome analysis identifies TNF superfamily receptors as potential therapeutic targets in alcoholic hepatitis","volume":"62","author":"S Affo","year":"2013","journal-title":"Gut"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.2217\/pgs.12.170","article-title":"Breaking free from the chains of pathway annotation: de novo pathway discovery for the analysis of disease processes","volume":"13","author":"B Lehne","year":"2012","journal-title":"Pharmacogenomics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref27","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":"ref28","doi-asserted-by":"crossref","first-page":"e6288","DOI":"10.1371\/journal.pone.0006288","article-title":"Layered functional network analysis of gene expression in human heart failure","volume":"4","author":"W Zhu","year":"2009","journal-title":"PLOS ONE"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-6-154","article-title":"Tools enabling the elucidation of molecular pathways active in human disease: application to hepatitis C virus infection","volume":"6","author":"DJ Reiss","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e1347","DOI":"10.1371\/journal.pone.0001347","article-title":"Linking gene expression and functional network data in human heart failure","volume":"2","author":"A Camargo","year":"2007","journal-title":"PLOS ONE"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/1752-0509-4-60","article-title":"Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network","volume":"4","author":"F Azuaje","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1161\/CIRCGENETICS.112.962977","article-title":"Systems-based approaches to cardiovascular biomarker discovery","volume":"5","author":"FJ Azuaje","year":"2012","journal-title":"Circ Cardiovasc Genet"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.gene.2012.03.039","article-title":"Systematic identification of common functional modules related to heart failure with different etiologies","volume":"499","author":"Y Xiao","year":"2012","journal-title":"Gene"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.gene.2013.08.027","article-title":"Insights into significant pathways and gene interaction networks underlying breast cancer cell line MCF-7 treated with 17beta-estradiol (E2)","volume":"533","author":"J Huan","year":"2014","journal-title":"Gene"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.2217\/14622416.7.7.1025","article-title":"Toxicogenomics in drug discovery and development: mechanistic analysis of compound\/class-dependent effects using the DrugMatrix database","volume":"7","author":"B Ganter","year":"2006","journal-title":"Pharmacogenomics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.febslet.2004.07.055","article-title":"Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments","volume":"573","author":"R Breitling","year":"2004","journal-title":"FEBS Lett"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2105-13-79","article-title":"Inferring high-confidence human protein-protein interactions","volume":"13","author":"X Yu","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref38","unstructured":"DrugMatrix (nd) National Institute of Environmental Health Sciences. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/ntp.niehs.nih.gov\/drugmatrix\/index.html\" xlink:type=\"simple\">https:\/\/ntp.niehs.nih.gov\/drugmatrix\/index.html<\/ext-link>."},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gng015","article-title":"Summaries of Affymetrix GeneChip probe level data","volume":"31","author":"RA Irizarry","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","article-title":"Affy \u2013 analysis of Affymetrix GeneChip data at the probe level","volume":"20","author":"L Gautier","year":"2004","journal-title":"Bioinformatics"},{"key":"ref41","unstructured":"R Development Core Team (2011) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\/\" xlink:type=\"simple\">http:\/\/www.R-project.org\/<\/ext-link>."},{"key":"ref42","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1093\/bioinformatics\/btn647","article-title":"ArrayQualityMetrics \u2013 a bioconductor package for quality assessment of microarray data","volume":"25","author":"A Kauffmann","year":"2009","journal-title":"Bioinformatics"},{"key":"ref43","unstructured":"Gentleman R, Carey V, Huber W, Hahne F (2013) genefilter: methods for filtering genes from microarray experiments, R. package version 1.40.0. Seattle, WA: Bioconductor. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/bioc.ism.ac.jp\/2.11\/bioc\/html\/genefilter.html\" xlink:type=\"simple\">http:\/\/bioc.ism.ac.jp\/2.11\/bioc\/html\/genefilter.html<\/ext-link>."},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2825","DOI":"10.1093\/bioinformatics\/btl476","article-title":"RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis","volume":"22","author":"F Hong","year":"2006","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e12145","DOI":"10.1371\/journal.pone.0012145","article-title":"Genome-wide gene expression analysis in response to organophosphorus pesticide chlorpyrifos and diazinon in <italic>C. elegans<\/italic>","volume":"5","author":"A Vinuela","year":"2010","journal-title":"PLOS ONE"},{"key":"ref46","first-page":"719","article-title":"Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics","volume":"24","author":"P Langfelder","year":"2008"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"DW Huang","year":"2009","journal-title":"Nat Protoc"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1186\/1471-2105-13-143","article-title":"QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence","volume":"13","author":"C Yu","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"D881","DOI":"10.1093\/nar\/gkr974","article-title":"The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse","volume":"40","author":"JT Eppig","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e24680","DOI":"10.1371\/journal.pone.0024680","article-title":"Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis","volume":"6","author":"J Zhang","year":"2011","journal-title":"PLOS ONE"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1039\/c2ib00133k","article-title":"Efficient key pathway mining: combining networks and OMICS data","volume":"4","author":"N Alcaraz","year":"2012","journal-title":"Integr Biol (Camb)"},{"key":"ref52","doi-asserted-by":"crossref","unstructured":"Baumbach J, Friedrich T, Kotzing T, Krohmer A, Muller J, et al. (2012) Efficient algorithms for extracting biological key pathways with global constraints. Proceedings of the 14th Annual Conference on Genetic and Evolutionary Computation. Philadelphia, Pennsylvania, USA: Association for Computing Machinery. pp. 169\u2013176.","DOI":"10.1145\/2330163.2330188"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nmeth.2212","article-title":"A travel guide to Cytoscape plugins","volume":"9","author":"R Saito","year":"2012","journal-title":"Nat Methods"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1706","DOI":"10.1016\/j.physa.2008.12.021","article-title":"Detect overlapping and hierarchical community structure in networks","volume":"388","author":"H Shen","year":"2009","journal-title":"Physica A"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"5060","DOI":"10.1073\/pnas.0511167103","article-title":"Galectin-3 regulates myofibroblast activation and hepatic fibrosis","volume":"103","author":"NC Henderson","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"e56009","DOI":"10.1371\/journal.pone.0056009","article-title":"Knowledge-based identification of soluble biomarkers: hepatic fibrosis in NAFLD as an example","volume":"8","author":"S Page","year":"2013","journal-title":"PLOS ONE"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"D1104","DOI":"10.1093\/nar\/gks994","article-title":"The Comparative Toxicogenomics Database: update 2013","volume":"41","author":"AP Davis","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"e21800","DOI":"10.1371\/journal.pone.0021800","article-title":"REVIGO summarizes and visualizes long lists of gene ontology terms","volume":"6","author":"F Supek","year":"2011","journal-title":"PLOS ONE"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1093\/bioinformatics\/bth078","article-title":"Open source clustering software","volume":"20","author":"MJ de Hoon","year":"2004","journal-title":"Bioinformatics"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1002\/hep.23421","article-title":"Ghrelin attenuates hepatocellular injury and liver fibrogenesis in rodents and influences fibrosis progression in humans","volume":"51","author":"M Moreno","year":"2010","journal-title":"Hepatology"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"8961","DOI":"10.1073\/pnas.0502674102","article-title":"Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays","volume":"102","author":"KH Pan","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/bib\/bbn001","article-title":"Gene-set approach for expression pattern analysis","volume":"9","author":"D Nam","year":"2008","journal-title":"Brief Bioinform"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1101\/gr.1910904","article-title":"Coexpression analysis of human genes across many microarray data sets","volume":"14","author":"HK Lee","year":"2004","journal-title":"Genome Res"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1074\/jbc.275.4.2247","article-title":"Molecular regulation of hepatic fibrosis, an integrated cellular response to tissue injury","volume":"275","author":"SL Friedman","year":"2000","journal-title":"J Biol Chem"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1755-1536-6-19","article-title":"Experimental liver fibrosis research: update on animal models, legal issues and translational aspects","volume":"6","author":"C Liedtke","year":"2013","journal-title":"Fibrogenesis Tissue Repair"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1111\/j.1478-3231.2012.02809.x","article-title":"Effect of RhoA on transforming growth factor beta1-induced rat hepatic stellate cell migration","volume":"32","author":"L Li","year":"2012","journal-title":"Liver Int"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1016\/S0002-9440(10)65683-0","article-title":"Expression of cellular prion protein in activated hepatic stellate cells","volume":"153","author":"K Ikeda","year":"1998","journal-title":"Am J Pathol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/S0168-8278(00)80306-2","article-title":"Clinicopathological characterization of prion: a novel marker of activated human hepatic stellate cells","volume":"33","author":"T Kitada","year":"2000","journal-title":"J Hepatol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1038\/nm.2807","article-title":"Mechanisms of fibrosis: therapeutic translation for fibrotic disease","volume":"18","author":"TA Wynn","year":"2012","journal-title":"Nat Med"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1016\/j.bbadis.2008.06.006","article-title":"Attenuated response to liver injury in moesin-deficient mice: impaired stellate cell migration and decreased fibrosis","volume":"1782","author":"T Okayama","year":"2008","journal-title":"Biochim Biophys Acta"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding challenges","volume":"8","author":"P Khatri","year":"2012","journal-title":"PLOS Comput Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"e13367","DOI":"10.1371\/journal.pone.0013367","article-title":"DEGAS: de novo discovery of dysregulated pathways in human diseases","volume":"5","author":"I Ulitsky","year":"2010","journal-title":"PLOS ONE"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1038\/labinvest.2012.121","article-title":"Lumican, an extracellular matrix proteoglycan, is a novel requisite for hepatic fibrosis","volume":"92","author":"A Krishnan","year":"2012","journal-title":"Lab Invest"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1172\/JCI66028","article-title":"Evolving therapies for liver fibrosis","volume":"123","author":"D Schuppan","year":"2013","journal-title":"J Clin Invest"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1016\/S0168-8278(99)80351-1","article-title":"Increased expression of plasminogen activator and plasminogen activator inhibitor during liver fibrogenesis of rats: role of stellate cells","volume":"31","author":"LP Zhang","year":"1999","journal-title":"J Hepatol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"C789","DOI":"10.1152\/ajpcell.00230.2013","article-title":"Cellular mechanisms of tissue fibrosis. 5. Novel insights into liver fibrosis","volume":"305","author":"A Mallat","year":"2013","journal-title":"Am J Physiol Cell Physiol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1016\/j.febslet.2007.02.064","article-title":"Legumain\/asparaginyl endopeptidase controls extracellular matrix remodeling through the degradation of fibronectin in mouse renal proximal tubular cells","volume":"581","author":"Y Morita","year":"2007","journal-title":"FEBS Lett"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s13105-011-0110-6","article-title":"Role of lipid droplet proteins in liver steatosis","volume":"67","author":"T Okumura","year":"2011","journal-title":"J Physiol Biochem"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"e71542","DOI":"10.1371\/journal.pone.0071542","article-title":"Crucial role of perilipin-3 (TIP47) in formation of lipid droplets and PGE2 production in HL-60-derived neutrophils","volume":"8","author":"F Nose","year":"2013","journal-title":"PLOS ONE"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1053\/hupa.2001.29675","article-title":"Vitronectin in the cirrhotic liver: an immunomarker of mature fibrosis","volume":"32","author":"GK Koukoulis","year":"2001","journal-title":"Hum Pathol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/S1350-9462(02)00010-1","article-title":"Myocilin and glaucoma: facts and ideas","volume":"21","author":"ER Tamm","year":"2002","journal-title":"Prog Retin Eye Res"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1080\/01926230601178207","article-title":"Gene expression analysis offers unique advantages to histopathology in liver biopsy evaluations","volume":"35","author":"AN Heinloth","year":"2007","journal-title":"Toxicol Pathol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"83","DOI":"10.14573\/altex.2011.2.083","article-title":"Food for Thought\u2026 on mapping the human toxome","volume":"28","author":"T Hartung","year":"2011","journal-title":"ALTEX"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.tox.2013.08.011","article-title":"The adverse outcome pathway concept: a pragmatic tool in toxicology","volume":"312","author":"M Vinken","year":"2013","journal-title":"Toxicology"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0112193","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T02:13:12Z","timestamp":1540260792000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0112193"}},"subtitle":[],"editor":[{"given":"Christina","family":"Chan","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,11,7]]},"references-count":85,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0112193","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,7]]}}}