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A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted.
Proper citation: SCPD - Saccharomyces cerevisiae promoter database (RRID:SCR_004412) Copy
http://llama.mshri.on.ca/funcassociate/
A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool
Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy
A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.
Proper citation: ADGO (RRID:SCR_006343) Copy
http://funspec.med.utoronto.ca/
FunSpec is a web-based tool for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms. FunSpec (an acronym for Functional Specification) inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list. The classes and categories evaluated were downloaded from the MIPS Database and the GO Database . In addition, many published datasets have been compiled to evaluate enrichment against. Hypertext links to the publications are given. The p-values, calculated using the hypergeometric distribution, represent the probability that the intersection of given list with any given functional category occurs by chance. The Bonferroni-correction divides the p-value threshold, that would be deemed significant for an individual test, by the number of tests conducted and thus accounts for spurious significance due to multiple testing over the categories of a database. After the Bonferroni correction, only those categories are displayed for which the chance probability of enrichment is lower than: p-value/#CD where #CD is the number of categories in the selected database. Without the Bonferroni Correction, all categories are displayed for which the same probability of enrichment is lower than: p-value threshold in an individual test Note that many genes are contained in many categories, especially in the MIPS database (which are hierarchical) and that this can create biases for which FunSpec currently makes no compensation. Also the databases are treated as independent from one another, which is really not the case, and each is searched seperately, which may not be optimal for statistical calculations. Nonetheless, we find it useful for sifting through the results of clustering analysis, TAP pulldowns, etc. Platform: Online tool
Proper citation: FunSpec (RRID:SCR_006952) Copy
http://gpcr.biocomp.unibo.it/bacello/
A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.
Proper citation: BaCelLo (RRID:SCR_011965) Copy
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