TY - JOUR
T1 - Mining human cancer datasets for kallikrein expression in cancer: The 'KLK-CANMAP' Shiny web tool
AU - Wang, Chenwei
AU - Moya, Leire
AU - Clements, Judith A.
AU - Nelson, Colleen C.
AU - Batra, Jyotsna
PY - 2018/7/27
Y1 - 2018/7/27
N2 - The dysregulation of the serine-protease family kallikreins (KLKs), comprising 15 genes, has been reportedly associated with cancer. Their expression in several tissues and physiological fluids makes them potential candidates as biomarkers and therapeutic targets. There are several databases available to mine gene expression in cancer, which often include clinical and pathological data. However, these platforms present some limitations when comparing a specific set of genes and can generate considerable unwanted data. Here, several datasets that showed significant differential expression (p<0.01) in cancer vs. normal (n=118), metastasis vs. primary (n=15) and association with cancer survival (n=21) have been compiled in a user-friendly format from two open and/or publicly available databases Oncomine and OncoLnc for the 15 KLKs. The data have been included in a free web application tool: the KLK-CANMAP https://cancerbioinformatics.shinyapps.io/klk-canmap/. This tool integrates, analyses and visualises data and it was developed with the R Shiny framework. Using KLK-CANMAP box-plots, heatmaps and Kaplan-Meier graphs can be generated for the KLKs of interest. We believe this new cancer KLK focused web tool will benefit the KLK community by narrowing the data visualisation to only the genes of interest. © 2018 Walter de Gruyter GmbH, Berlin/Boston.
AB - The dysregulation of the serine-protease family kallikreins (KLKs), comprising 15 genes, has been reportedly associated with cancer. Their expression in several tissues and physiological fluids makes them potential candidates as biomarkers and therapeutic targets. There are several databases available to mine gene expression in cancer, which often include clinical and pathological data. However, these platforms present some limitations when comparing a specific set of genes and can generate considerable unwanted data. Here, several datasets that showed significant differential expression (p<0.01) in cancer vs. normal (n=118), metastasis vs. primary (n=15) and association with cancer survival (n=21) have been compiled in a user-friendly format from two open and/or publicly available databases Oncomine and OncoLnc for the 15 KLKs. The data have been included in a free web application tool: the KLK-CANMAP https://cancerbioinformatics.shinyapps.io/klk-canmap/. This tool integrates, analyses and visualises data and it was developed with the R Shiny framework. Using KLK-CANMAP box-plots, heatmaps and Kaplan-Meier graphs can be generated for the KLKs of interest. We believe this new cancer KLK focused web tool will benefit the KLK community by narrowing the data visualisation to only the genes of interest. © 2018 Walter de Gruyter GmbH, Berlin/Boston.
UR - http://www.scopus.com/inward/record.url?scp=85050912130&partnerID=8YFLogxK
U2 - 10.1515/hsz-2017-0322
DO - 10.1515/hsz-2017-0322
M3 - Article
C2 - 30052511
AN - SCOPUS:85050912130
SN - 1431-6730
VL - 399
SP - 983
EP - 995
JO - Biological Chemistry
JF - Biological Chemistry
IS - 9
ER -
