PhD Scientific Days 2024

Poster Session J - Pathological and Oncological Sciences 1.

Development of a Web Application for Analysis of DNA Methylation in Colorectal Adenocarcinoma Coupled with Clinical Data

Előadó neve

Ms. Müller, Dalma

Neptun code

ZHUJHN

Előadó munkahelye

Semmelweis University, Department of Bioinformatics

Előadó telefonszáma

06702132172

Előadó e-mail címe

dalma.muller2@gmail.com

Az előadás címe

Development of a Web Application for Analysis of DNA Methylation in Colorectal Adenocarcinoma Coupled with Clinical Data

Szerző(k) neve és munkahelye

Dalma Müller¹, Balázs Győrffy¹

1: Semmelweis University

Bemutatás módja

Poszter

Szekció

Poster Session J - Pathological and Oncological Sciences 1.

Language of the presentation

English

Preferred session

Pathological and Oncological Sciences

Összefoglaló szövege

Aim. Genome-wide methylation studies advance the understanding of colorectal adenocarcinoma progression and the identification of novel biomarkers. Our goal was to assemble an integrated database containing Illumina HumanMethylation450K data from normal colon, colon adenoma, and colon adenocarcinoma tissues. In order to enable comfortable examination of the database we also aim to create a web-based interactive platform.
Methods. Data were downloaded from the GEO (Gene Expression Omnibus) database. Raw files were processed in R using the minfi and the wateRmelon libraries. To identify differentially methylated regions, gene level analysis was performed and the different regions were compared using a Kruskal-Wallis-test. Most promising biomarker candidates identified through ROC analysis were further analyzed on CpG level. For web application development we used the shiny R package.
Results. The established database contains 2,646 samples derived from 1,940 patients assembled from 17 data bases. Samples were split into test and training sets and the analysis proved to have robust final results with a 88.27% average overlap between the identified significantly differentially methylated genes. Tissue sets including and without normal tissues from colorectal cancer patients were separately analyzed. Normal tissues from healthy subjects had more, but less cancer specific differentially methylated genes compared to CRC samples, than all normal tissues with the exception of the 3’UTR region. . The top-ranking genes of our analysis included TMEM240, ACTBL2, and SPAG4L. The established platform can be accessed at epigenplot.com, and entails three features: comparison of methylation levels across genes and gene regions (e.g., first exon, 5'UTR), visualization of methylation levels for all CpGs within a gene, and the analysis of the top genes of a given KEGG pathway respectively.
Conclusion. We assembled a sizeable database containing colorectal samples with genome-wide methylation data and established a pipeline for data processing. Our results confirm that changes in DNA-methylation are early events of colorectal cancer development. Our database could be a useful starting point for biomarker discovery and the web platform will serve the efficient exploration of the assembled data.

University

Semmelweis University

Supervisor

Balázs Győrffy

Publication of my abstract

I do not give consent to the publication of my abstract on the website of the congress.

Kind

Szabad

Status

elfogadva

Accepted presentation method

poszter

Előadás fájl jóváhagyás

nem rendelkezett róla

Előadó

6817

Start

16:45

End

16:48