Preservation affinity in consensus modules among stages of HIV-1 progression

BMC Bioinformatics

Methodology Article

Sumanta Ray¹  Sk Md Mosaddek Hossain¹  Anirban Mukhopadhyay² 

[1] Department of Computer Science and Engineering, Aliah University, Kolkata, 700156, West Bengal, India;Department of Computer Science and Engineering, University of Kalyani, Kalyani, 741235, West Bengal, India;

关键词: Gene co-expression network;    Module eigengene;    Hierarchical clustering;    Consensus modules;    Immune regulatory genes;   

DOI  :  10.1186/s12859-017-1590-3

 received in 2016-10-01, accepted in 2017-03-09,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAnalysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding.MethodsHIV-1 disease provides a well-documented progression pattern through three stages of infection: acute, chronic and non-progressor. In this article, we have developed a novel framework to describe the relationship among the consensus (or shared) co-expression modules for each pair of HIV-1 infection stages. The consensus modules are identified to assess the preservation of network properties. We have investigated the preservation patterns of co-expression networks during HIV-1 disease progression through an eigengene-based approach.ResultsWe discovered that the expression patterns of consensus modules have a strong preservation during the transitions of three infection stages. In particular, it is noticed that between acute and non-progressor stages the preservation is slightly more than the other pair of stages. Moreover, we have constructed eigengene networks for the identified consensus modules and observed the preservation structure among them. Some consensus modules are marked as preserved in two pairs of stages and are analyzed further to form a higher order meta-network consisting of a group of preserved modules. Additionally, we observed that module membership (MM) values of genes within a module are consistent with the preservation characteristics. The MM values of genes within a pair of preserved modules show strong correlation patterns across two infection stages.ConclusionsWe have performed an extensive analysis to discover preservation pattern of co-expression network constructed from microarray gene expression data of three different HIV-1 progression stages. The preservation pattern is investigated through identification of consensus modules in each pair of infection stages. It is observed that the preservation of the expression pattern of consensus modules remains more prominent during the transition of infection from acute stage to non-progressor stage. Additionally, we observed that the module membership values of genes are coherent with preserved modules across the HIV-1 progression stages.

【 授权许可】

CC BY   
© The Author(s) 2017

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