the Open Access publication charges for this article was provided by NSF-ITR Grant-0428344. Conﬂict of interest statement. None declared. REFERENCES 1. Fire,A., Montgomery,M.K., Kostas,S.A., Driver,S.E. and Mello,C.C. (1998) Potent and speciﬁc genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811. 2. Girard,L.R., Fiedler,T.J., Harris,T.W., Carvalho,F., Antoshechkin,I., Han,M., Sternberg,P.W., Stein,L.D. and Chalﬁe,M. (2007) WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res., 35, D472–D475. 3. Jin,Y., Murali,T.M. and Ramakrishnan,N. (2007) Compositional Mining of Multi-Relational Biological Datasets. Tech. Report., TR- 07-29, Computer Science, Virginia Tech. http://eprints.cs.vt.edu/ archive/00000988/ 4. Grothaus,G. (2005) Biologically-Interpretable Disease Classiﬁcation Based on Gene Expression Data. Master’s thesis, 2005, etd-05272005- 145543, Virginia Polytechnic Institute and State University, http:// scholar.lib.vt.edu/theses/available/etd-05272005-145543/. 5. Tanay,A., Sharan,R. and Shamir,R. (2002) Discovering statistically signiﬁcant biclusters in gene expression data. Bioinformatics, 18, S136–S144. 6. Bergmann,S., Ihmels,J. and Barkai,N. (2003) Iterative signature algorithm for the analysis of large-scale gene expression data. Phys. Rev. E., 67, 031902. 7. Agrawal,R., Gehrke,J., Gunopulos,D. and Raghavan,P. (2005) Automatic subspace clustering of high dimensional data. Data Mining Knowledge Discov., 11, 5–33. 8. Hsiao,C.J. and Zaki,M.J. (2005) Eﬃcient algorithms for mining closed item sets and their lattice structure. IEEE Trans. Knowledge Data Eng., 17, 462–478. 9. Nanopoulos,A. and Manolopoulos,Y. (2002) Eﬃcient similarity search for market basket data. VLDB J., 11, 138–152. 10. Sarawagi,S. and Kirpal,A. (2004) Eﬃcient set joins on similarity predicates. In Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD’04), Paris, France, ACM, New York, pp. 743–754. 11. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235–242. 12. Symersky,J., Zhang,Y., Schormann,N., Li,S., Bunzel,R., Pruett,P., Luan,C.H. and Luo,M. (2004) Structural genomics of Caenorhabditis elegans: structure of the BAG domain. Acta Crystallogr. D Biol. Crystallogr., 60, 1606–1610. 13. Stark,C., Breitkreutz,B.J., Reguly,T., Boucher,L., Breitkreutz,A. and Tyers,M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535. 14. Ball,C.A., Awad,I.A., Demeter,J., Gollub,J., Hebert,J.M., Hernandez-Boussard,T., Jin,H., Matese,J.C., Nitzberg,M. et al. (2005) The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res., 33, D580–D582. 15. Sonnichsen,B., Koski,L.B., Walsh,A., Marschall,P., Neumann,B., Brehm,M., Alleaume,A.M., Artelt,J., Bettencourt,P. et al. (2005) Full-genome RNAi proﬁling of early embryogenesis in Caenorhabditis elegans. Nature, 434, 462–469. 16. Groth,P., Pavlova,N., Kalev,I., Tonov,S., Georgiev,G., Pohlenz,H.D. and Weiss,B. (2007) PhenomicDB: a new cross-species genotype/ phenotype resource. Nucleic Acids Res., 35, D696–D699. 17. Maeda,I., Kohara,Y., Yamamoto,M. and Sugimoto,A. (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol., 11, 171–176. 18. Cho,S., Rogers,K.W. and Fay,D.S. (2007) The C. elegans glycopeptide hormone receptor ortholog, FSHR-1, regulates germline diﬀerentiation and survival. Curr. Biol., 17, 203–212. 19. Cram,E.J., Shang,H. and Schwarzbauer,J.E. (2006) A systematic RNA interference screen reveals a cell migration gene network in C. elegans. J. Cell Sci., 119, 4811–4818. 20. Curran,S.P. and Ruvkun,G. (2007) Lifespan regulation by evolu- tionarily conserved genes essential for viability. PLoS Genet., 3, e56. Nucleic Acids Research, 2008, Vol. 36, Database issue D75 21. Frand,A.R., Russel,S. and Ruvkun,G. (2005) Functional genomic analysis of C. elegans molting. PLoS Biol., 3, e312. 22. Govindan,J.A., Cheng,H., Harris,J.E. and Greenstein,D. (2006) G-alpha o/i and G-alpha s signaling function in parallel with the MSP/Eph receptor to control meiotic diapause in C. elegans. Curr. Biol., 16, 1257–1268. 23. Hamilton,B., Dong,Y., Shindo,M., Liu,W., Odell,I., Ruvkun,G. and Lee,S.S. (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev., 19, 1544–1555. 24. Hansen,M., Taubert,S., Crawford,D., Libina,N., Lee,S.J. and Kenyon,C. (2007) Lifespan extension by conditions that inhibit translation in Caenorhabditis elegans. Aging Cell, 6, 95–110. 25. Lamitina,T., Huang,C.G. and Strange,K. (2006) Genome-wide RNAi screening identiﬁes protein damage as a regulator of osmoprotective gene expression. Proc. Natl Acad. Sci. USA, 103, 12173–12178. 26. Lettre,G., Kritikou,E.A., Jaeggi,M., Calixto,A., Fraser,A.G., Kamath,R.S., Ahringer,J. and Hengartner,M.O. (2004) Genome-wide RNAi identiﬁes p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death Diﬀer., 11, 1198–1203. 27. Nollen,E.A., Garcia,S.M., van Haaften,G., Kim,S., Chavez,A., Morimoto,R.I. and Plasterk,R.H. (2004) Genome-wide RNA interference screen identiﬁes previously undescribed regulators of polyglutamine aggregation. Proc. Natl Acad. Sci. USA, 101, 6403–6408. 28. Pothof,J., van Haaften,G., Thijssen,K., Kamath,R.S., Fraser,A.G., Ahringer,J., Plasterk,R.H. and Tijsterman,M. (2003) Identiﬁcation of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev., 17, 443–448. 29. Poulin,G., Dong,Y., Fraser,A.G., Hopper,N.A. and Ahringer,J. (2005) Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans. EMBO J., 24, 2613–2623. 30. Saleh,M.C., van Rij,R.P., Hekele,A., Gillis,A., Foley,E., O’Farrell,P.H. and Andino,R. (2006) The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing. Nat. Cell Biol., 8, 793–802. 31. Schmitz,C., Kinge,P. and Hutter,H. (2007) Axon guidance genes identiﬁed in a large-scale RNAi screen using the RNAi-hypersen- sitive Caenorhabditis elegans strain nre-1(hd20) lin-15b(hd126). Proc. Natl Acad. Sci. USA, 104, 834–839. 32. Sieburth,D., Chong,Q., Dybbs,M., Tavazoie,M., Kennedy,S., Wang,D., Dupuy,D., Rual,J.F., Hill,D.E. et al. (2005) Systematic analysis of genes required for synapse structure and function. Nature, 436, 510–517. 33. Stein,K.K., Davis,E.S., Hays,T. and Golden,A. (2007) Components of the spindle assembly checkpoint regulate the anaphase-promoting complex during meiosis in Caenorhabditis elegans. Genetics, 175, 107–123. 34. Suzuki,Y. and Han,M. (2006) Genetic redundancy masks diverse functions of the tumor suppressor gene PTEN during C. elegans development. Genes Dev., 20, 423–428. 35. van Haaften,G., Vastenhouw,N.L., Nollen,E.A., Plasterk,R.H. and Tijsterman,M. (2004) Gene interactions in the DNA damage- response pathway identiﬁed by genome-wide RNA-interference analysis of synthetic lethality. Proc. Natl Acad. Sci. USA, 101, 12992–12996. 36. Vastenhouw,N.L., Fischer,S.E., Robert,V.J., Thijssen,K.L., Fraser,A.G., Kamath,R.S., Ahringer,J. and Plasterk,R.H. (2003) A genome-wide screen identiﬁes 27 genes involved in transposon silencing in C. elegans. Curr. Biol., 13, 1311–1316. 37. Madeira,S.C. and Oliveira,A.L. (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans. Comput. Biol. Bioinform., 1, 24–45. 38. Zaki,M.J. and Hsiao,C.J. (1999) CHARM: an eﬃcient algorithm for closed itemset mining. SIAM Int. Conf. Data Mining, Tech. Report., RPI, 1999, 457–473, http://citeseer.ist.psu.edu/ zaki99charm.html. 39. Crittenden,S.L., Rudel,D., Binder,J., Evans,T.C. and Kimble,J. (1997) Genes required for GLP-1 asymmetry in the early Caenorhabditis elegans embryo. Dev. Biol., 181, 36–46.