Open Access Highly Accessed Research article

Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs

Perry Evans1, William Dampier2, Lyle Ungar1 and Aydin Tozeren2*

1 Genomics and Computational Biology and Department of Computer and Information Science, University of Pennsylvania, Levine Hall, 3330 Walnut Street, Philadelphia, PA 19104, USA

2 Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone 714, 3120 Market Street, Philadelphia, PA 19104, USA

For all author emails, please log on.

BMC Medical Genomics 2009, 2:27 doi:10.1186/1755-8794-2-27

Published: 18 May 2009

Additional files

Additional file 1:

Number of sequences in HIV-1 protein alignments. For each HIV-1 protein, we list the number of sequences used in the study.

Format: XLS Size: 107KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

ELMs and CDs. For each ELM-CD pair, the fraction of human proteins with each is listed along with the fraction of HPRD linked proteins that have the ELM-CD relation.

Format: XLS Size: 110KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Comparison of H1 and DHHE for each HIV-1 protein. H1 and DHHE are compared for all HIV-1 proteins, giving the overlap (Match) between the two protein sets. P-values are calculated as the probability of matching Match genes or more when comparing DHHE and H1 drawn from the 5954 proteins in the study (see Methods).

Format: XLS Size: 8KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Comparison of HHP and HHE for KEGG proteins for each HIV-1 protein. HHP and HHE are compared for all HIV-1 proteins when HHP is restricted to genes in all KEGG pathways, and KEGG pathways enriched (p-value < 0.01, see Methods) with HHP. P-values are calculated as the probability of matching Match genes or more when comparing HHE and HHP drawn from the 5954 proteins in the study (see Methods).

Format: TAB Size: 1KB Download file

Open Data

Additional file 5:

H1 and H2 for each HIV-1 protein. This table gives HHP as H1-H2 Entrez GeneID pairs for each HIV-1 protein. Proteins in HHE are marked with *, proteins in HHP KEGG enriched pathways are marked with +, and proteins in both are marked with **.

Format: XLS Size: 3.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data