ABSTRACT
Understanding the regulation of gene expression is critical to many areas of biology while control via RNAs has found considerable interest as a tool for scientific discovery and potential therapeutic applications. For example whole genome RNA interference (RNAi) screens and whole proteome scans provide views of how the entire transcriptome or proteome responds to biological, chemical or environmental perturbations of a gene's activity. Small RNA (sRNA) or MicroRNA (miRNA) are known to regulate pathways and bind mRNA, while the function of miRNAs discovered in experimental studies is often unknown. In both cases, RNAi and miRNA require labor intensive studies to tease out their functions within gene networks. Available software to analyze relationships is currently an ad hoc and often a manual process that can take up to several hours to analyze a single candidate RNAi or miRNA. With experiments frequently highlighting tens to hundreds of candidates this represents a considerable bottleneck. We suggest there is a gap in miRNA and RNAi research caused by inadequate current software that could be improved. For example a new software application could be created that provides interactive, comprehensive target analysis that leverages past datasets to lead to statistically stronger analyses.
Subject(s)
MicroRNAs/genetics , RNA Interference , Software , Animals , Databases, Genetic , Genomics/methods , HumansABSTRACT
SUMMARY: The NetAffx Gene Ontology (GO) Mining Tool is a web-based, interactive tool that permits traversal of the GO graph in the context of microarray data. It accepts a list of Affymetrix probe sets and renders a GO graph as a heat map colored according to significance measurements. The rendered graph is interactive, with nodes linked to public web sites and to lists of the relevant probe sets. The GO Mining Tool provides visualization combining biological annotation with expression data, encompassing thousands of genes in one interactive view. AVAILABILITY: GO Mining Tool is freely available at http://www.affymetrix.com/analysis/query/go_analysis.affx
Subject(s)
Algorithms , Documentation/methods , Information Storage and Retrieval/methods , Natural Language Processing , Oligonucleotide Array Sequence Analysis , Software , User-Computer Interface , Abstracting and Indexing/methods , Computer Graphics , Database Management Systems , Gene Expression Profiling/methodsABSTRACT
GPCR-GRAPA-LIB is a library of HMMs describing G protein coupled receptor families. These families are initially defined by class of receptor ligand, with divergent families divided into subfamilies using phylogenic analysis and knowledge of GPCR function. Protein sequences are applied to the models with the GRAPA curve-based selection criteria. RefSeq sequences for Homo sapiens, Drosophila melanogaster, and Caenorhabditis elegans have been annotated using this approach.
Subject(s)
Databases, Protein , GTP-Binding Proteins/chemistry , GTP-Binding Proteins/genetics , Models, Genetic , Models, Statistical , Sequence Alignment/methods , Sequence Analysis, Protein/methods , Algorithms , Amino Acid Sequence , Documentation , Evolution, Molecular , GTP-Binding Proteins/classification , Molecular Sequence Data , Structure-Activity RelationshipABSTRACT
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix. For each probeset, NetAffx lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context. Sequence annotations include Gene Ontology (GO) terms and depiction of GO graph relationships; predicted protein domains and motifs; orthologous sequences; links to relevant pathways; and links to public databases including UniGene, LocusLink, SWISS-PROT and OMIM.
