Supplemental Figure 4 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

Newton, Yulia; Novak, Adam M.; Swatloski, Teresa; McColl, Duncan C.; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S.; Baertsch, Robert; Salama, Sofie R.; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C.; Haussler, David; Morozova, Olena; Stuart, Joshua M.

doi:10.1158/0008-5472.22419030.v1

Supplemental Figure 4 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

journal contribution

posted on 2023-03-31, 01:46 authored by Yulia Newton, Adam M. Novak, Teresa Swatloski, Duncan C. McColl, Sahil Chopra, Kiley Graim, Alana S. Weinstein, Robert Baertsch, Sofie R. Salama, Kyle Ellrott, Manu Chopra, Theodore C. Goldstein, David Haussler, Olena Morozova, Joshua M. Stuart

Enrichment of Immune signaling in the integrated pan-cancer cluster. Different level of evidence support the association of the integrated pan-cancer cluster with an immune phenotype. (A) Enrichment of T- and B-cell signaling shown on the integrated map, yellow gradient (see Supplemental Methods). (B) Enrichment of high ESTIMATE scores in the pan-cancer samples, waterfall plot with pan-cancer cluster samples in red. (C) Enrichment of the immune-related pathways identified by differential expression analysis. (D) Unsupervised analysis of master regulator activities inferred by the MARINa method. Gene clusters enriched for T- and B-cell signaling, interferon signaling, and TNFA via NFKB signaling, red font. (E) The top enriched pathways based on the output of master regulator scores derived with MARINa are immune-related. (F) Copy number events in the integrated pan-cancer cluster compared to other samples in the full cohort. The pan-cancer cluster shows a lower number of copy number events in both arm-level events and focal events. Arm-level events (pan-cancer group on the right, background cohort on the left). (G) Same as F but focal events (pan-cancer group on the right, background cohort on the left). (H) Purity estimates in the integrated pan-cancer cluster compared to all other samples in the cohort. The pan-cancer cluster (green box) shows lower purity when compared to the whole cohort as a background (yellow box). This finding is consistent with other analyses indicating high immune signaling in the pan-cancer cluster.

Funding

National Cancer Institute

National Human Genome Research Institute

National Institute for General Medical Sciences

National Science Foundation Office of Cyberinfrastructure CAREER

Cancer – Prostate Cancer Foundation Prostate Dream Team

St. Baldricks Foundation Treehouse Childhood Cancer

California Kids Cancer Comparison

History

ARTICLE ABSTRACT

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex “omics” data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111–4. ©2017 AACR.