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. 2021 Dec 14;22:592. doi: 10.1186/s12859-021-04505-w

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© The Author(s) 2021

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Biological implication of subnetworks in the context of pathway. A Subnetworks from TCGA-LUAD (TCGA Lung Adenocarcinoma) are mapped to the RAS pathway. Genes colored in red are present in the COSMIC Cancer Gene Census. Blue oval: genes in KRAS-SHC3; Red oval: genes in BRCA2-FANCA. B Subnetworks from TCGA-BRCA (TCGA Breast Invasive Carcinoma) are mapped to the RAS pathway and associated with survival. Red oval: genes in ERBB2-FGFR2; Blue oval: genes in BRAF-SCRIB; Yellow oval: genes in BRCA2-FANCA. P-values are combined p-values from gene-pair fisher’s tests. The KM-plot of survival analysis is obtained from the comparison of mutated vs. non-mutated samples for four genes in the subnetwork ERBB2-FGFR2. Coxph p-values adjusted by sex and age for both single gene and a group by subnetwork genes are shown in the table