{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T14:29:54Z","timestamp":1776954594412,"version":"3.51.4"},"reference-count":34,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,6,21]],"date-time":"2020-06-21T00:00:00Z","timestamp":1592697600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2019M3A9H1030682"],"award-info":[{"award-number":["2019M3A9H1030682"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"abstract":"<jats:p>The complexity of interstitial cystitis\/bladder pain syndrome (IC\/BPS) has led to considerable uncertainty in terms of diagnosis and prevalence of the condition. Here, we try to identify the IC\/BPS-associated genes through an integrated analysis of Gene Expression Omnibus (GEO) datasets and confirm experimentally to predict the pathologic diagnosis of IC\/BPS. Data mining analysis of GEO datasets (GSE621, GSE11783, GSE28242, and GSE57560) revealed a total of 53 (51 upregulated and two downregulated) common differentially expressed genes (DEGs) in IC\/BPS. A protein\u2013protein interaction (PPI) network was then constructed with the 53 common DEGs using Cytoscape v3.7.2, and subsequently, six hub genes (CD5, CD38, ITGAL, IL7R, KLRB1, and IL7R) were identified using cytoHubba v0.1 that were upregulated in IC\/BPS. Enrichment analysis of common DEGs revealed that hematopoietic cell lineage, immune system, and T-cell receptor (TCR) signaling in na\u00efve CD4+ T cell signaling pathways were prominently involved with the common 51 upregulated DEGs. The two common downregulated DEGs may enrich linoleic acid metabolism and synthesis of epoxy (EET) and dihydroxyeicosatrienoic acid (DHET) signaling pathways in IC\/BPS. Moreover, our RT-PCR data confirmed that the expression of the five hub genes (CD38, ITGAL, IL7R, KLRB1, and IL7R) was significantly augmented in IC\/BPS patients\u2019 samples when compared with their normal counterparts. In this study, we systematically predict the significant biomarkers and possible signaling pathways involved in IC\/BPS, confirming the differential expression of the hub genes in tissue samples from patients with IC\/BPS. Thus, the hub genes might be used as potential diagnostic biomarkers of IC\/BPS.<\/jats:p>","DOI":"10.3390\/jcm9061935","type":"journal-article","created":{"date-parts":[[2020,6,24]],"date-time":"2020-06-24T07:14:19Z","timestamp":1592982859000},"page":"1935","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis\/Bladder Pain Syndrome with Hunner Lesion"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1325-3499","authenticated-orcid":false,"given":"Subbroto Kumar","family":"Saha","sequence":"first","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8431-2831","authenticated-orcid":false,"given":"Tak-Il","family":"Jeon","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6491-0252","authenticated-orcid":false,"given":"Soo Bin","family":"Jang","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Se Jong","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyung Min","family":"Lim","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu Jin","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyeong Gon","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Urology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aram","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Urology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0968-7932","authenticated-orcid":false,"given":"Ssang-Goo","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biotechnology, Molecular &amp; Cellular Reprogramming Center (MCRC), and Incurable Disease Animal Model &amp; Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,6,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1016\/j.juro.2011.03.064","article-title":"AUA Guideline for the Diagnosis and Treatment of Interstitial Cystitis\/Bladder Pain Syndrome","volume":"185","author":"Hanno","year":"2011","journal-title":"J. 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