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

Contact Author: Yanjun Qi (




Validation of Predictions:



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



          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)




















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[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.