OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

JCO Clinical Cancer Informatics
Hayley M DingerdissenRaja Mazumder

Abstract

The purpose of OncoMX1 knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types. Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker data were integrated, unified by relevant biomedical ontologies, and subjected to rule-based automated quality control before ingestion into the database. OncoMX provides integrated data encompassing more than 1,000 unique biomarker entries (939 from the Early Detection Research Network [EDRN] and 96 from the US Food and Drug Administration) mapped to 20,576 genes that have either mutation or differential expression in cancer. Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both human genes and their mouse orthologs. OncoMX has prioritized user feedback as a means of guiding development priorities. By mapping to and integrating data from several cancer ge...Continue Reading

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Citations

Sep 2, 2020·JCO Clinical Cancer Informatics·Jeremy L Warner, Juli D Klemm
Nov 28, 2020·Nucleic Acids Research·David S WishartMichael Wilson
Apr 30, 2020·Cancer Letters·Sanjay GuptaShashank Kumar
Mar 31, 2021·Database : the Journal of Biological Databases and Curation·Janisha A PatelJonathon Keeney
Apr 1, 2021·Briefings in Functional Genomics·Harpreet KaurGajendra P S Raghava
May 21, 2021·Briefings in Bioinformatics·Nikhita GogateRaja Mazumder

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Methods Mentioned

BETA
scRNA sequencing
Assay
xenograft

Software Mentioned

DEXTER Extraction Association to Diseases ( DiMeX )
jQuery
CentOS Linux
OncoMX
iPTMnet
TCPA
DEXTER
MariaDB
HemOnc
DESeq2

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