Semi-Supervised Multi-Task Learning for Predicting Interactions between HIV-1 and Human Proteins

 
Contact Author: Yanjun Qi (qyj@cs.cmu.edu)

 

 

 

Validation of Predictions:

 

 

          The top ranked predicted HIV-Human interaction pairs (cutoff score -1.5) from model EMBO.

          HIVPPI.embOmodel.all.ave.cutList.cvs

 

          We compared the top ranked predicted HIV-Human PPI pairs with the partial positive pairs from GROUP1+GROUP2

          We also compared those human genes in the top ranked predicted HIV-Human PPI pairs to two extra human gene list

          282 human genes that have been reported in the siRNA screen to have an effect on HIV-1 infection upon silencing [1]

          316 human proteins highjacked by HIV-1 in its virion [5]

          1049 human genes that have been reported by one of the siRNA functional screens published recently [1,2,3,4].

          All these three human gene lists used in validations could be downloaded here !

 

 

Score cutoff

Predicted Interactions

Interaction Confirmed by Partial Positive

Novel Interactions

Human Gene in Predicted Interactions

Confirmed with siRNA (282 genes)

Confirmed with Virion (316 genes)

Combined Four siRNA set

(1049 genes)

-1.8

3428

259

3123

1027

24

72

96

-1.5

2434

223

2172

721

21

61

72

 

 

 

[1].Brass, A.L., Dykxhoorn, D.M., Benita, Y., Yan, N., Engelman, A., Xavier, R.J., Lieberman, J., and Elledge, S.J. (2008). Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen. Science.

 

[2]. Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., et al. (2008). Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135, 49-60.

 

[3]. Yeung, M.L., Houzet, L., Yedavalli, V.S., and Jeang, K.T. (2009). A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. J Biol Chem 284, 19463-19473.

 

[4]. Zhou, H., Xu, M., Huang, Q., Gates, A.T., Zhang, X.D., Castle, J.C., Stec, E., Ferrer, M., Strulovici, B., Hazuda, D.J., et al. (2008). Genome-scale RNAi screen for host factors required for HIV replication. Cell host & microbe 4, 495-504.

 

[5] Ott, D. E. (2008). Cellular proteins detected in hiv-1. Rev Med Virol , 18(3), 159–175.