Cargando…
Pan-cancer mapping of differential protein-protein interactions
Deciphering the variations in the protein interactome is required to reach a systems-level understanding of tumorigenesis. To accomplish this task, we have considered the clinical and transcriptome data on >6000 samples from The Cancer Genome Atlas for 12 different cancers. Utilizing the gene exp...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039988/ https://www.ncbi.nlm.nih.gov/pubmed/32094374 http://dx.doi.org/10.1038/s41598-020-60127-x |
_version_ | 1783500896371474432 |
---|---|
author | Gulfidan, Gizem Turanli, Beste Beklen, Hande Sinha, Raghu Arga, Kazim Yalcin |
author_facet | Gulfidan, Gizem Turanli, Beste Beklen, Hande Sinha, Raghu Arga, Kazim Yalcin |
author_sort | Gulfidan, Gizem |
collection | PubMed |
description | Deciphering the variations in the protein interactome is required to reach a systems-level understanding of tumorigenesis. To accomplish this task, we have considered the clinical and transcriptome data on >6000 samples from The Cancer Genome Atlas for 12 different cancers. Utilizing the gene expression levels as a proxy, we have identified the differential protein-protein interactions in each cancer type and presented a differential view of human protein interactome among the cancers. We clearly demonstrate that a certain fraction of proteins differentially interacts in the cancers, but there was no general protein interactome profile that applied to all cancers. The analysis also provided the characterization of differentially interacting proteins (DIPs) representing significant changes in their interaction patterns during tumorigenesis. In addition, DIP-centered protein modules with high diagnostic and prognostic performances were generated, which might potentially be valuable in not only understanding tumorigenesis, but also developing effective diagnosis, prognosis, and treatment strategies. |
format | Online Article Text |
id | pubmed-7039988 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70399882020-02-28 Pan-cancer mapping of differential protein-protein interactions Gulfidan, Gizem Turanli, Beste Beklen, Hande Sinha, Raghu Arga, Kazim Yalcin Sci Rep Article Deciphering the variations in the protein interactome is required to reach a systems-level understanding of tumorigenesis. To accomplish this task, we have considered the clinical and transcriptome data on >6000 samples from The Cancer Genome Atlas for 12 different cancers. Utilizing the gene expression levels as a proxy, we have identified the differential protein-protein interactions in each cancer type and presented a differential view of human protein interactome among the cancers. We clearly demonstrate that a certain fraction of proteins differentially interacts in the cancers, but there was no general protein interactome profile that applied to all cancers. The analysis also provided the characterization of differentially interacting proteins (DIPs) representing significant changes in their interaction patterns during tumorigenesis. In addition, DIP-centered protein modules with high diagnostic and prognostic performances were generated, which might potentially be valuable in not only understanding tumorigenesis, but also developing effective diagnosis, prognosis, and treatment strategies. Nature Publishing Group UK 2020-02-24 /pmc/articles/PMC7039988/ /pubmed/32094374 http://dx.doi.org/10.1038/s41598-020-60127-x Text en © The Author(s) 2020 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/. |
spellingShingle | Article Gulfidan, Gizem Turanli, Beste Beklen, Hande Sinha, Raghu Arga, Kazim Yalcin Pan-cancer mapping of differential protein-protein interactions |
title | Pan-cancer mapping of differential protein-protein interactions |
title_full | Pan-cancer mapping of differential protein-protein interactions |
title_fullStr | Pan-cancer mapping of differential protein-protein interactions |
title_full_unstemmed | Pan-cancer mapping of differential protein-protein interactions |
title_short | Pan-cancer mapping of differential protein-protein interactions |
title_sort | pan-cancer mapping of differential protein-protein interactions |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039988/ https://www.ncbi.nlm.nih.gov/pubmed/32094374 http://dx.doi.org/10.1038/s41598-020-60127-x |
work_keys_str_mv | AT gulfidangizem pancancermappingofdifferentialproteinproteininteractions AT turanlibeste pancancermappingofdifferentialproteinproteininteractions AT beklenhande pancancermappingofdifferentialproteinproteininteractions AT sinharaghu pancancermappingofdifferentialproteinproteininteractions AT argakazimyalcin pancancermappingofdifferentialproteinproteininteractions |