Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2018 Nov 12;9:4746. doi: 10.1038/s41467-018-07021-3

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 4 — Clinical association of breast cancer biomarkers. a Heatmap of patients’ risk scores estimated using top n_Breast=50 subnetworks in the Metabric validation cohort. Column covariates show patient classifications based on PAM50-based molecular subtypes and SIMMS predicted risk groups. Row covariates indicate functional class of subnetwork’s originating pathway. Columns and rows were clustered using divisive clustering. Number in parenthesis of y-axis labels represents subnetwork number from a given pathway; with details in subnetwork database (SIMMS R package). ‘Fc Epsilon Receptor I Signaling in Mast Cells’ is repeated twice because it is represented by two different pathways in the database (ID = 100165 and ID = 200003 in subnetworks database; SIMMS R package). b Clustered (divisive) heatmap of correlation (Spearman) between patients using their subnetwork risk score profiles (top n_Breast=50 subnetworks) in the Metabric validation cohort with covariates as detailed in a. c Forest plot showing HR and 95% CI (multivariate Cox proportional hazards model) of the breast cancer subtype-specific markers, as well as cross-platform validation. Datasets originating from Illumina (ILMN) and Affymetrix (AFFY) were used in turn for cross platform training and validation. Due to limited availability of clinical annotations on Affymetrix based cohorts, only the Illumina dataset (Metabric) was used for subtype-specific models. For these, the Metabric-published training and validation cohorts were maintained for training and validation purposes. Numbers in parenthesis indicate the size of the validation cohort. Asterisks represent statistical significance of differential outcome between the predicted low-risk and high-risk groups (*P < 0.05, **P < 0.01, ***P < 0.001, Wald-test)