NDLI: Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis

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Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis

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Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis

Content Provider	ACM Digital Library
Author	Zeng, Tao Chen, Luonan Wang, Ziming
Abstract	Motivation: In recent disease study, many key pathogen genes/proteins are found to have not significant differential expressions, and thus, they tend to be disregarded in conventional differential expression analysis or network analysis. Meanwhile, the activity in dry-experiment rather than expression in wet-experiment have been proposed to effectively estimate the actual regulation power of such important biomolecules, e.g. transcriptional factors. But, it is still unknown what and how a hidden factor (e.g. phosphorylation) determines this kind of virtual regulation power as activity [1]. Especially, for the cancer development study, it is emergent to reconstruct the active protein interaction network and detect the underlying phosphorylation pattern in a dynamic manner [2-7]. Methods: Based on the c-Myc mouse model of liver cancer, we have first collected protein expression and protein phosphorylation data at several developmental time points. Then, we constructed a rough protein interaction network as background by conditional mutual information. Next, we improved the conventional network component analysis on its robustness, and used this advanced approach RNCA (Robust Network Component Analysis) to reconstruct the time-dependent protein interaction networks and estimate the activity of target protein at different times simultaneously. Finally, considering the different experiment-qualities of protein expression and phosphorylation data, we used canonical correlation analysis to detect the maximal correlation between the expression and phosphorylation of a group of proteins (e.g. protein network module), which could reveal the active protein sub-network and its determinate factor as phosphorylation. Results: In the preliminary study, we have evaluated the robustness of RNCA by comparing with other conventional methods. And on the real biological data, we have found the rewired protein interaction network during cancer development, its corresponding active proteins, and their drivers as protein phosphorylation. This work can be further used in early diagnosis of diseases by edge biomarkers [1-2], network biomarkers [3-4] and dynamical network biomarkers [5-7].
Starting Page	49
Ending Page	49
Page Count	1
File Format	PDF
ISBN	9781450312752
DOI	10.1145/2665970.2665991
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-11-07
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Cancer development Phosphorylation Protein interaction network Network component analysis Activity
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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