D72 Nucleic Acids Research, 2008, Vol. 36, Database issue overlapping biclusters, which can be organized alongside a lattice of subset relationships. The SAMBA algorithm casts biclustering as a problem of ﬁnding bicliques in a bipartite graph. Given an edge- weighted graph (e.g. between genes and experiments labeled with expression levels) SAMBA detects dense sub- graphs, which are then iteratively improved (using local addition/removal of vertices) in a post-processing phase. Biclusters are connected if the overlap between the participating entities satisﬁed a Jaccard’s threshold of 0.5. Chains computed in this manner all mediate through the gene entity set, since it serves a central role in CMGSDB (i.e. all relationships involve genes). Patterns mined by CDM serve many purposes. For instance, they can be used to impute functions and properties to unannotated genes, they can make unex- pected connections between upstream and downstream indicators, and they can summarize the distribution of data in the database more succinctly by identifying the sets of entities that dominate in many compositions. QUERYING CMGSDB The CMGSDB consists of a web interface and a PostgreSQL database management system. The web interface has been implemented using static and dynamic HTML, PHP, CSS and JavaScript. PostgreSQL is used to store the data described in the previous section and in Figure 2. The web interface of CMGSDB can be used for querying. The user can search against all C. elegans biots. Genes, for example, can be searched using names, loci, transcript IDs and annotations. A biot page, apart from displaying basic information about that biot, also displays relationships with other biots that have been captured within CMGSDB. For instance, the phenotype page not only displays phenotype description, ID and source, but also shows existing relationships with other phenotypes, GO categories associated with the phenotype, RNAi experiments in which the phenotype was observed, genes whose knockdown resulted in the phenotype, and chains in which the phenotype participates. Biot pages are closely interlinked through biot IDs. As far as possible, biots are hyperlinked on pages. A biot page also contains hyperlinks to Wormbase and GO wherever applicable. Figure 3 illustrates the page for the gpr-1 gene through a screenshot. Chains, as described before, are available for searching and browsing. Chains can be queried by participating genes, number of common genes among all biclusters and number of biclusters. A chain with three biclusters containing gene glp-1 is shown in Table 1. LIN-12/Notch signaling In C. elegans, the LIN-12/Notch protein family mediates cell–cell interactions. Glp-1 and lin-12 encode two proteins in the LIN-12/Notch pathway, which is conserved in mammalian development. The two general cell–cell inter- actions that determine cell fate and involve these proteins Figure 3. Screenshot of the gene page. are lateral speciﬁcation and induction. Querying CMGSDB for glp-1 gives two chains (chain 153 and chain 154). Table 1 illustrates chain 153, which demon- strates a chain of three (two non-trivial) biclusters. The biclusters with the GO categories and RNAi phenotypes