{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:04:23Z","timestamp":1790687063176,"version":"4.1.0"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2014,5,1]],"date-time":"2014-05-01T00:00:00Z","timestamp":1398902400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0096153","type":"journal-article","created":{"date-parts":[[2014,5,1]],"date-time":"2014-05-01T20:49:08Z","timestamp":1398977348000},"page":"e96153","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci"],"prefix":"10.1371","volume":"9","author":[{"given":"Christopher J.","family":"Cardinale","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junfei","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengnan","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert N.","family":"Baldassano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Struan F. A.","family":"Grant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hakon","family":"Hakonarson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,5,1]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"e199","DOI":"10.1371\/journal.pmed.0020199","article-title":"Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays","volume":"2","author":"CM Costello","year":"2005","journal-title":"PLoS Med"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1002\/ibd.20879","article-title":"Diagnosis of ulcerative colitis before onset of inflammation by multivariate modeling of genome-wide gene expression data","volume":"15","author":"J Olsen","year":"2009","journal-title":"Inflamm Bowel Dis"},{"key":"ref3","doi-asserted-by":"crossref","unstructured":"Planell N, Lozano JJ, Mora-Buch R, Masamunt MC, Jimeno M, <etal>et al<\/etal>.. (2012) Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations. Gut.","DOI":"10.1136\/gutjnl-2012-303333"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1002\/ibd.20110","article-title":"Genome-wide gene expression differences in Crohn&apos;s disease and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis","volume":"13","author":"F Wu","year":"2007","journal-title":"Inflamm Bowel Dis"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"L Jostins","year":"2012","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/35079107","article-title":"Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn&apos;s disease","volume":"411","author":"JP Hugot","year":"2001","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/35079114","article-title":"A frameshift mutation in NOD2 associated with susceptibility to Crohn&apos;s disease","volume":"411","author":"Y Ogura","year":"2001","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1126\/science.1135245","article-title":"A genome-wide association study identifies IL23R as an inflammatory bowel disease gene","volume":"314","author":"RH Duerr","year":"2006","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/ng1954","article-title":"A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1","volume":"39","author":"J Hampe","year":"2007","journal-title":"Nat Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature05911","article-title":"Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls","volume":"447","year":"2007","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/ng.764","article-title":"Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47","volume":"43","author":"CA Anderson","year":"2011","journal-title":"Nat Genet"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1038\/ng.717","article-title":"Genome-wide meta-analysis increases to 71 the number of confirmed Crohn&apos;s disease susceptibility loci","volume":"42","author":"A Franke","year":"2010","journal-title":"Nat Genet"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.ajhg.2009.01.026","article-title":"Diverse genome-wide association studies associate the IL12\/IL23 pathway with Crohn Disease","volume":"84","author":"K Wang","year":"2009","journal-title":"Am J Hum Genet"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1136\/gut.2009.199679","article-title":"New IBD genetics: common pathways with other diseases","volume":"60","author":"CW Lees","year":"2011","journal-title":"Gut"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1053\/j.gastro.2011.02.048","article-title":"Autophagy, microbial sensing, endoplasmic reticulum stress, and epithelial function in inflammatory bowel disease","volume":"140","author":"A Kaser","year":"2011","journal-title":"Gastroenterology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/ng.203","article-title":"Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease","volume":"40","author":"S Kugathasan","year":"2008","journal-title":"Nat Genet"},{"key":"ref17","unstructured":"Affymetrix I (2006) Guide to Probe Logarithmic Intensity Error (PLIER) Estimation."},{"key":"ref18","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1186\/1471-2105-7-395","article-title":"Probe set algorithms: is there a rational best bet?","volume":"7","author":"J Seo","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"Article3","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"GK Smyth","year":"2004","journal-title":"Stat Appl Genet Mol Biol"},{"key":"ref20","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":"ref21","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"MT Maurano","year":"2012","journal-title":"Science"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e1000294","DOI":"10.1371\/journal.pbio.1000294","article-title":"Rare variants create synthetic genome-wide associations","volume":"8","author":"SP Dickson","year":"2010","journal-title":"PLoS Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1016\/j.ajhg.2010.04.003","article-title":"Interpretation of association signals and identification of causal variants from genome-wide association studies","volume":"86","author":"K Wang","year":"2010","journal-title":"Am J Hum Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1152\/physiolgenomics.2000.4.1.1","article-title":"Analysis of mucosal gene expression in inflammatory bowel disease by parallel oligonucleotide arrays","volume":"4","author":"BK Dieckgraefe","year":"2000","journal-title":"Physiol Genomics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1093\/hmg\/10.5.445","article-title":"Ulcerative colitis and Crohn&apos;s disease: distinctive gene expression profiles and novel susceptibility candidate genes","volume":"10","author":"IC Lawrance","year":"2001","journal-title":"Hum Mol Genet"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1111\/j.1365-2036.2005.02443.x","article-title":"Inflammatory gene signature in ulcerative colitis with cDNA macroarray analysis","volume":"21","author":"S Okahara","year":"2005","journal-title":"Aliment Pharmacol Ther"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e56818","DOI":"10.1371\/journal.pone.0056818","article-title":"Whole genome gene expression meta-analysis of inflammatory bowel disease colon mucosa demonstrates lack of major differences between Crohn&apos;s disease and ulcerative colitis","volume":"8","author":"A Granlund","year":"2013","journal-title":"PLoS One"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1086\/522374","article-title":"Pathway-based approaches for analysis of genomewide association studies","volume":"81","author":"K Wang","year":"2007","journal-title":"Am J Hum Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/nrg2884","article-title":"Analysing biological pathways in genome-wide association studies","volume":"11","author":"K Wang","year":"2010","journal-title":"Nat Rev Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"S Purcell","year":"2007","journal-title":"Am J Hum Genet"},{"key":"ref31","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":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B-Methodological"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0096153","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,26]],"date-time":"2024-05-26T08:42:36Z","timestamp":1716712956000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0096153"}},"subtitle":[],"editor":[{"given":"Cormac T.","family":"Taylor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,5,1]]},"references-count":31,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2014,5,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0096153","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,1]]}}}