Protocol to set up the CellMinerCDB pharmacogenomics analysis web application with custom cell line data

Fathi Elloumi; Camille Tlemsani; Christine M Heske; Lorinc Pongor; Prashant Khandagale; Sudhir Varma; Paul S Meltzer; Javed Khan; William C Reinhold; Yves Pommier; Augustin Luna

doi:10.1016/j.xpro.2025.104076

Protocol to set up the CellMinerCDB pharmacogenomics analysis web application with custom cell line data

STAR Protoc. 2025 Dec 19;6(4):104076. doi: 10.1016/j.xpro.2025.104076. Epub 2025 Sep 24.

Authors

Affiliations

¹ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address: fathi.elloumi@nih.gov.
² Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Medical Oncology, Cochin Hospital, Paris Cancer Institute CARPEM, Université Paris Cité, APHP Centre, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR8104, Paris Cancer Institute CARPEM, Université Paris Cité, Paris, France.
³ Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁴ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Hungarian Centre of Excellence for Molecular Medicine, Cancer Genomics and Epigenetics Core Group, Szeged, Hungary.
⁵ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
⁶ Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
⁷ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Computational Biology Branch, Division of Intramural Research, National Library of Medicine, NIH, Bethesda, MD 20892, USA. Electronic address: augustin@nih.gov.

Abstract

CellMiner Cross-Database (CellMinerCDB) is an interactive web application for integrating and analyzing molecular and pharmacological data across human cancer cell lines. Here, we detail the setup process, including installing necessary software, preparing compatible datasets, and customizing configuration files; we use sarcoma data as an example. The protocol involves data loading, software configuration, and deployment to enable univariate and multivariate analyses. For complete details on the use and execution of this protocol, please refer to Luna et al.¹ and Tlemsani et al.².

Keywords: Bioinformatics; Cancer; Genomics; Health Sciences.

Published by Elsevier Inc.

MeSH terms

Cell Line, Tumor
Computational Biology* / methods
Humans
Internet
Pharmacogenetics* / methods
Software*