PhenoPred web site provides two basic services: (i) for a given Disease Ontology (DO) term, PhenoPred will rank genes that are most likely to be associated with this term; and (ii) for a given gene it ranks DO terms that are most likely to be associated with a query gene. PhenoPred works with 422 DO terms, which were selected using the following rules: (i) each DO term has to be associated with at least 10 genes, (ii) if two DO terms are associated with the same set of genes and one term is a descendent of the other, the node closer to the root of DO is eliminated; (iii) nodes directly descending from the root node are eliminated on the basis that they are too general (e.g. DOID: 7 is "disease of anatomical entity").

Diseases and genes of known genetic involvement were extracted from OMIM (Hamosh, et al., 2000), Swiss-Prot (Bairoch, et al., 2005) and HPRD (Peri, et al., 2003). PPI interaction map was assembled by combining the physical interaction data from HPRD, OPHID (Brown and Jurisica, 2005) and studies by Rual et al. (2005) and Stezl et al. (2005). Collected disease names and associated genes were manually integrated into DO. Datasets can be downloaded here.

Sean D. Mooney
Center for Computational Biology and Bioinformatics
Indiana University School of Medicine
410 W. 10th Street., Suite 5000
Indianapolis, IN 46202

Predrag Radivojac
School of Informatics
Indiana University
901 E. 10th Street
Bloomington, IN 47408

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Brown, K.R. and Jurisica, I. (2005) Online predicted human interaction database, Bioinformatics, 21, 2076-2082.

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Peri, S., Navarro, J.D., Amanchy, R., Kristiansen, T.Z., Jonnalagadda, C.K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T.K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H.N., Rashmi, B.P., Ramya, M.A., Zhao, Z., Chandrika, K.N., Padma, N., Harsha, H.C., Yatish, A.J., Kavitha, M.P., Menezes, M., Choudhury, D.R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S.K., Madavan, V., Joseph, A., Wong, G.W., Schiemann, W.P., Constantinescu, S.N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G.C., Dang, C.V., Garcia, J.G., Pevsner, J., Jensen, O.N., Roepstorff, P., Deshpande, K.S., Chinnaiyan, A.M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans, Genome Res, 13, 2363-2371.

Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P. and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network, Nature, 437, 1173-1178.

Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H. and Wanker, E.E. (2005) A human protein-protein interaction network: a resource for annotating the proteome, Cell , 122, 957-968.