ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma

Asna Tungekar, Sumana Mandarthi, Pooja Rajendra Mandaviya, Veerendra P Gadekar, Ananthajith Tantry, Sowmya Kotian, Jyotshna Reddy, Divya Prabha, Sushma Bhat, Sweta Sahay, Roshan Mascarenhas, Raghavendra Rao Badkillaya, Manoj Kumar Nagasampige, Mohan Yelnadu, Harsh Pawar, Prashantha Hebbar, Manoj Kumar Kashyap

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.

Original languageEnglish
Article number12715
Pages (from-to)12715
Number of pages15
JournalScientific Reports
Volume8
Issue number1
DOIs
Publication statusPublished - 24 Aug 2018

Keywords

  • BARRETTS-ESOPHAGUS
  • CANCER
  • CPG ISLAND HYPERMETHYLATION
  • FALSE DISCOVERY RATE
  • GENE-EXPRESSION PROFILES
  • GROWTH-FACTOR RECEPTOR
  • PATHWAY GENES
  • RISK-FACTORS
  • SINGLE NUCLEOTIDE POLYMORPHISMS
  • UP-REGULATION

Cite this

Tungekar, A., Mandarthi, S., Mandaviya, P. R., Gadekar, V. P., Tantry, A., Kotian, S., Reddy, J., Prabha, D., Bhat, S., Sahay, S., Mascarenhas, R., Badkillaya, R. R., Nagasampige, M. K., Yelnadu, M., Pawar, H., Hebbar, P., & Kashyap, M. K. (2018). ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Scientific Reports, 8(1), 12715. [12715]. https://doi.org/10.1038/s41598-018-30579-3