Abstract
This study was conducted to identify genes that are differentially expressed in paracancerous tissue and to determine the potential predictive value of selected gene panel. Gene transcriptome data of bladder tissue was downloaded from UCSC Xena browser and NCBI GEO repository, including GTEx (the Genotype-Tissue Expression project) data, TCGA (The Cancer Genome Atlas) data, and GEO (Gene Expression Omnibus) data. Differentially Expressed Genes (DEGs) analysis was performed to identify tumor-DEGs candidate genes, using the intersection of tumor-paracancerous DEGs genes and paracancerous-normal DEGs genes. The survival-related genes were screened by Kaplan-Meier (KM) survival analysis and univariable Cox regression with the cutoff criteria of KM < 0.05 and cox p-value < 0.05. The risk model was developed using Lasso regression. The clinical data were analyzed by univariate and multivariate Cox regression analysis. Gene Ontology (GO) and KEGG enrichment analysis were performed in the DEGs genes between the high-risk and low-risk subgroups. We identified six survival-related genes, EMP1, TPM1, NRP2, FGFR1, CAVIN1, and LATS2, found in the DEG analyses of both, tumor-paracancerous and paracancerous-normal differentially expressed dat...Continue Reading
References
Apr 1, 1982·Radiology·J A Hanley, B J McNeil
Jul 6, 2000·Biometrics·P J HeagertyM S Pepe
Aug 6, 2005·Bioinformatics·Steffen DurinckWolfgang Huber
Nov 27, 2008·Nucleic Acids Research·Da Wei HuangRichard A Lempicki
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
May 22, 2009·Cancer Research·Darren C TomlinsonMargaret A Knowles
Jul 21, 2009·Nature Protocols·Steffen DurinckWolfgang Huber
Nov 17, 2009·Bioinformatics·Mark D RobinsonGordon K Smyth
Apr 30, 2010·Bioinformatics·Matthew D Wilkerson, D Neil Hayes
Sep 3, 2010·PloS One·Carmen J MarsitKarl T Kelsey
Oct 27, 2010·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Vera L CostaGuro E Lind
Jan 31, 2012·Nucleic Acids Research·Davis J McCarthyGordon K Smyth
Mar 19, 2013·BMC Bioinformatics·Charlotte Soneson, Mauro Delorenzi
Sep 24, 2013·Urologic Oncology·Evanguelos XylinasShahrokh F Shariat
Nov 15, 2013·Bioinformatics·Yang LiaoWei Shi
May 28, 2014·International Journal of Cancer. Journal International Du Cancer·B KeckM H Muders
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Aug 8, 2015·Scientific Reports·Ke-Hung TsuiHorng-Heng Juang
Mar 14, 2017·Journal of Drug Targeting·Binqiang TianYonghui Li
Oct 24, 2017·Nature Communications·Dvir AranAtul J Butte
Jul 25, 2018·Molecular Cancer·Yi PanKa Fai To
Aug 17, 2018·Cancer Research·Sohini RoyKaustubh Datta
Sep 13, 2018·CA: a Cancer Journal for Clinicians·Freddie BrayAhmedin Jemal
Nov 25, 2018·Journal of Cellular Physiology·Nazi AghaalikhaniMarzieh Mahmoodi
Dec 17, 2018·European Urology·F Johannes P van ValenbergJ Alfred Witjes
Jan 1, 2019·Current Biology : CB·Valentina RauschCarsten G Hansen
Jan 15, 2019·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Alvaro Quintanal-VillalongaLuis Paz-Ares
May 22, 2019·Journal of Cellular Biochemistry·Junxiang WangYouxin Zhou
Nov 24, 2019·Oncology Research·Rena AbuliziChuan-Guang Zhang
Apr 8, 2020·Clinical Laboratory·Li HuZhi-Long Yan