Journal Article

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

Laufer, Itay, Netanely, Dvir, Stern, Neta, Shamir, Ron

2019

Overview

Background Analysis of large genomic datasets along with their accompanying clinical information has shown great promise in cancer research over the last decade. Such datasets typically include thousands of samples, each measured by one or several high-throughput technologies (‘omics’) and annotated with extensive clinical information. While instrumental for fulfilling the promise of personalized medicine, the analysis and visualization of such large datasets is challenging and necessitates programming skills and familiarity with a large array of software tools to be used for the various steps of the analysis. Results We developed PROMO (Profiler of Multi-Omic data), a friendly, fully interactive stand-alone software for analyzing large genomic cancer datasets together with their associated clinical information. The tool provides an array of built-in methods and algorithms for importing, preprocessing, visualizing, clustering, clinical label enrichment testing, and survival analysis that can be performed on a single or multi-omic dataset. The tool can be used for quick exploration and stratification of tumor samples taken from patients into clinically significant molecular subtypes. Identification of prognostic biomarkers and generation of simple subtype classifiers are additional important features. We review PROMO’s main features and demonstrate its analysis capabilities on a breast cancer cohort from TCGA. Conclusions PROMO provides a single integrated solution for swiftly performing a complete analysis of cancer genomic data for subtype discovery and biomarker identification without writing a single line of code, and can, therefore, make the analysis of these data much easier for cancer biologists and biomedical researchers. PROMO is freely available for download at http://acgt.cs.tau.ac.il/promo/ .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Arrays / Bioinformatics / Biological markers / Biomarkers / Biomedical and Life Sciences / Breast cancer / Cancer / Cancer biomarkers / Cancer genomics / Cancer subtypes / Clustering / Comparative genomics / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer programming / Computer programs / Criminal investigation / Datasets / DNA methylation / Downloading / Familiarity / Gene expression / Genomics / Genomics - methods / Humans / Life Sciences / Microarrays / Multi-omic clustering / Multi-omics / Neoplasms - genetics / Personalized medicine / Pharmacogenomics / Precision medicine / Software / Software development tools / Survival analysis / Technology / Tumors / User interface / Visualization