Open Access Research article

MicroRNA regulation and its effects on cellular transcriptome in Human Immunodeficiency Virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts

Karolina Duskova1, Pruthvi Nagilla1, Hai-Son Le2, Priyadarshini Iyer1, Anbupalam Thalamuthu3, Jeremy Martinson1, Ziv Bar-Joseph2, William Buchanan1, Charles Rinaldo1 and Velpandi Ayyavoo1*

Author Affiliations

1 Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA, 15261, USA

2 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA

3 Human Genetics, Genome Institute of Singapore, 60 Biopolis Street 02-01, Singapore, Singapore

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BMC Infectious Diseases 2013, 13:250  doi:10.1186/1471-2334-13-250

Published: 30 May 2013

Additional files

Additional file 1: Table S1:

Differentially regulated miRNA in low and high viral load groups compared to uninfected control group using.

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Additional file 2: Figure S1:

Hierarchical clustering of miRNAs in HIV-1 infected low viral load (LVL) versus high viral load (HVL) subjects. The dendogram depicting the clustering of samples is calculated using Complete linkage with Euclidian distance measure values. Color ranging from green to red indicates minimum to maximum dCT. Numbers on Xaxis represent subject group. The clustergrams were generated using data from StatMiner analyses.

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Additional file 3: Table S2:

Differentially regulated mRNA probes in low (LVL) and high viral load (HVL) groups compared to uninfected control group with statistical significance.

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Additional file 4: Figure S2:

Hierarchical clustering of differentially regulated mRNA in low viral load (LVL) ompared to high viral load (HVL) subjects. The probes in this clustergram are significantly differentially regulated (p < 0.05). Red indicates high, blue indicates low, and gray stands for no change in level of expression. Numbers on X-axis represent subject group; Y-axis represents the gene symbol.

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Additional file 5: Table S3:

a: Top ten Canonical pathways representing mRNA that are differentially expressed in LVL group compared to uninfected seronegative subjects. b: Top ten Canonical pathways representing mRNA that are differentially expressed in HVL group compared to uninfected seronegative subjects.

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Additional file 6: Figure S3:

Network of predicted miRNA-mRNA interactions by GroupMiR using results from miRNA and mRNA array and visualized by Cytoscape. Regression-based method was used to predict the potential miRNA (circles) that actively regulate mRNA (squares). Differentially regulated miRNA and mRNA in HIV-1 infected subjects compared to the uninfected controls were used to predict the miRNA-mRNA pairs. Red and green within the mRNA represents up and down regulation, respectively. Each slice within the circle represents HIV-1 infected subject.

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