Module Based Differential Coexpression Analysis Method for Type 2 Diabetes

BioMed Research International
Lin YuanDe-Shuang Huang

Abstract

More and more studies have shown that many complex diseases are contributed jointly by alterations of numerous genes. Genes often coordinate together as a functional biological pathway or network and are highly correlated. Differential coexpression analysis, as a more comprehensive technique to the differential expression analysis, was raised to research gene regulatory networks and biological pathways of phenotypic changes through measuring gene correlation changes between disease and normal conditions. In this paper, we propose a gene differential coexpression analysis algorithm in the level of gene sets and apply the algorithm to a publicly available type 2 diabetes (T2D) expression dataset. Firstly, we calculate coexpression biweight midcorrelation coefficients between all gene pairs. Then, we select informative correlation pairs using the "differential coexpression threshold" strategy. Finally, we identify the differential coexpression gene modules using maximum clique concept and k-clique algorithm. We apply the proposed differential coexpression analysis method on simulated data and T2D data. Two differential coexpression gene modules about T2D were detected, which should be useful for exploring the biological function o...Continue Reading

References

Oct 16, 1999·Science·A L Barabasi, R Albert
Jan 5, 2000·Proceedings of the National Academy of Sciences of the United States of America·M P BrownD Haussler
Feb 12, 2002·Bioinformatics·Alexander SturnZlatko Trajanoski
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·M Girvan, M E J Newman
Jan 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Richard M Shiffrin, Katy Börner
Jun 3, 2004·Genome Research·Homin K LeePaul Pavlidis
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman
Jul 21, 2004·Bioinformatics·Dennis Kostka, Rainer Spang
May 21, 2005·Physical Review Letters·Imre DerényiTamás Vicsek
Dec 22, 2005·Nature Reviews. Genetics·David B AllisonMahyar Sabripour
Aug 8, 2006·Journal of Biochemistry and Molecular Biology·Lisa L NguyenGareth S Denyer
Nov 30, 2006·Molecular Systems Biology·John RachlinSimon Kasif
Aug 2, 2007·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Tova F FullerSteve Horvath
May 13, 2010·BMC Bioinformatics·Johannes M FreudenbergMario Medvedovic
Oct 20, 2010·Current Hypertension Reports·Silvia Sookoian, Carlos J Pirola

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE3068

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.