157 467

Cited 0 times in

Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection

DC Field Value Language
dc.contributor.authorYoon, DY-
dc.contributor.authorKim, HS-
dc.contributor.authorSuh-Kim, H-
dc.contributor.authorPark, RW-
dc.contributor.authorLee, K-
dc.description.abstractBACKGROUND: Microarray analyses based on differentially expressed genes (DEGs) have been widely used to distinguish samples across different cellular conditions. However, studies based on DEGs have not been able to clearly determine significant differences between samples of pathophysiologically similar HIV-1 stages, e.g., between acute and chronic progressive (or AIDS) or between uninfected and clinically latent stages. We here suggest a novel approach to allow such discrimination based on stage-specific genetic features of HIV-1 infection. Our approach is based on co-expression changes of genes known to interact. The method can identify a genetic signature for a single sample as contrasted with existing protein-protein-based analyses with correlational designs.

METHODS: Our approach distinguishes each sample using differentially co-expressed interacting protein pairs (DEPs) based on co-expression scores of individual interacting pairs within a sample. The co-expression score has positive value if two genes in a sample are simultaneously up-regulated or down-regulated. And the score has higher absolute value if expression-changing ratios are similar between the two genes. We compared characteristics of DEPs with that of DEGs by evaluating their usefulness in separation of HIV-1 stage. And we identified DEP-based network-modules and their gene-ontology enrichment to find out the HIV-1 stage-specific gene signature.

RESULTS: Based on the DEP approach, we observed clear separation among samples from distinct HIV-1 stages using clustering and principal component analyses. Moreover, the discrimination power of DEPs on the samples (70–100% accuracy) was much higher than that of DEGs (35–45%) using several well-known classifiers. DEP-based network analysis also revealed the HIV-1 stage-specific network modules; the main biological processes were related to “translation,” “RNA splicing,” “mRNA, RNA, and nucleic acid transport,” and “DNA metabolism.” Through the HIV-1 stage-related modules, changing stage-specific patterns of protein interactions could be observed.

CONCLUSIONS: DEP-based method discriminated the HIV-1 infection stages clearly, and revealed a HIV-1 stage-specific gene signature. The proposed DEP-based method might complement existing DEG-based approaches in various microarray expression analyses.
dc.titleDifferentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection-
dc.contributor.affiliatedAuthor서, 해영-
dc.contributor.affiliatedAuthor박, 래웅-
dc.contributor.affiliatedAuthor이, 기영-
dc.type.localJournal Papers-
dc.citation.titleBMC systems biology-
dc.citation.numberSuppl 2-
dc.identifier.bibliographicCitationBMC systems biology, 5(Suppl 2):S1-S1, 2011-
Appears in Collections:
Journal Papers > School of Medicine / Graduate School of Medicine > Medical Informatics
Journal Papers > School of Medicine / Graduate School of Medicine > Anatomy
Files in This Item:
There are no files associated with this item.


해당 아이템을 이메일로 공유하기 원하시면 인증을 거치시기 바랍니다.

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.