Software
GeneMerge
GeneMerge is a versatile genomics program that can be used to analyze a wide range of functional genomic data. In particular GeneMerge is useful for the analysis of microarray data and other large biological datasets. GeneMerge returns functional and categorical genomic data for a given set of genes and provides statistical rank scores for over-representation of particular functions or categories in the dataset. Given a set of genes, GeneMerge can tell you, for example, whether these genes are statistically over-represented in a particular functional or biochemical class, clustered in a region of the genome, or are associated with a particular RNAi or deletion phenotype.
SSClust
Smoothing Spline Clustering is a statistical method for clustering time-series gene expression data. In particular, SSClust is useful for clustering genes in microarray experiments performed over several time-points, for example, over the course of development, a drug treatment, or other temporally based experiments. Smoothing Spline Clustering provides clusters of similarly expressed genes using a statistically rigorous, biologically based, data-driven method. Importantly, SSC provides the number of gene clusters in a given dataset without an a priori specification of the genes that belong to each cluster, a mean curve for each cluster describing the average expression profile of each cluster, and associated 95% confidence bands.
Shared Motif Method
The Shared Motif Method is a sequence alignment algorithm designed to measure the extent of functionally relevant cis-regulatory sequence change in noncoding in the proximity of homologous genes. Because small intrachromosomal rearrangements resulting in changes in cis-acting element order, orientation and spacing can occur over moderate stretches of evolutionary time, while leaving gene expression patterns intact (Ludwig et al. 2000), the SMM discovers regions of local similarity between DNA sequences without respect to their order, orientation, or spacing.