This talk is an activity from the FEBS Junior Section, an initiative set up by students and young researchers from some of the FEBS Constituent Societies. Each month members of the FEBS Junior Section organize an online event on either a research or a career topic. This talk was coordinated by the Junior-TBS, the Junior Section of the Turkish Biochemical Society (TBS).

Speaker: Dr H. Atakan Ekiz from Izmir Institute of Technology (IzTech) in İzmir, Türkiye.
Topic: "TCGEx – Democratizing cancer transcriptomics analysis with an interactive bioinformatics platform".
Date and time: 11 April 2025, 17:00 CEST.
Registration link: https://us06web.zoom.us/webinar/register/WN_3IWLBMP6SC6Feo8ZzStnZA.

Biosketch

Dr H. Atakan Ekiz is an Assistant Professor at the Izmir Institute of Technology (IzTech) İzmir, Türkiye, leading the Tumor Immunology and Bioinformatics Laboratory. Dr Ekiz earned his PhD in Oncological Sciences (Molecular Biology) and MSc in Clinical Investigation from the University of Utah (USA), supported by a Fulbright Scholarship. His lab integrates high-throughput data analysis, functional genomics, and computational modeling to identify novel immune biomarkers and therapeutic targets with a particular focus on noncoding RNAs. He has received multiple prestigious awards, including the EMBO Installation Grant, Turkish Academy of Sciences Outstanding Young Investigator Award, and Turkish Immunology Society’s Işıl Berat Barlan Award. His ongoing projects funded by several organizations focus on immune checkpoint regulation, lncRNA-mediated interferon signaling, and the development of peptide inhibitors for cancer immunotherapy. He also collaborates internationally on single-cell RNA sequencing, immunotherapy response prediction, and computational oncology. Dr. Ekiz is actively involved in scientific mentorship and education, recognized with awards for Best Course Design and Best Educator. Through his research and interdisciplinary collaborations, he aims to bridge the gap between basic cancer immunology and translational medicine.

Abstract

High-throughput transcriptomic data holds great promise for understanding cancer biology, yet its complexity often necessitates advanced computational skills, creating barriers for many researchers. To address this, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform that enables interactive analysis of cancer transcriptomics data without requiring programming expertise. Built on the R/Shiny framework, TCGEx integrates preprocessed TCGA datasets, immune checkpoint inhibition studies, and user-uploaded data, allowing for survival modeling, gene set enrichment analysis, unsupervised clustering, and machine learning-based biomarker discovery.

Using TCGEx, we identified microRNAs associated with intratumoral immunity and validated their clinical relevance with independent immunotherapy trial datasets. Additionally, we uncovered a cytokine gene signature predictive of immune checkpoint inhibitor response across multiple cancers. The platform's modular design supports diverse research applications, facilitating data-driven hypothesis generation and accelerating translational oncology efforts.

TCGEx is freely available at https://tcgex.iyte.edu.tr, empowering researchers to explore and visualize cancer transcriptomics data through an intuitive, interactive interface. This talk will showcase TCGEx’s key analytical capabilities and its role in democratizing bioinformatics.

The FEBS Junior Section

Want to join this platform for young European life scientists?  Learn more about our initiative, check out the Room for the FEBS Junior Section and – if you do not have a junior section yet – read this post about how to set one up!

Photo by Mariola Grobelska on Unsplash.