Coexpression analysis is a powerful, widely used methodology for the investigation of underlying patterns in gene expression data. This "guilt-by-association" approach aims to find groups of genes with closely correlated expression profiles. Observation of consistent correlations across phenotypically diverse samples indicates that these genes have a shared function.
Provides normal brain expression levels and coexpression analysis results for reference. BrainEXP provides an in-depth analysis based on the largest sample sizes. It provides three types of charts: (i) the differential expression analysis, (ii) the gene expression in different brain regions and sexes shown by boxplot, and (iii) the gene expression in different brain regions and ages demonstrated by scatterplot.
A coexpression database for plant species, which provides a parallel view of multiple coexpression data sets with network analysis tools. The user can effectively find functional gene relationships and design experiments to confirm the gene functions by reverse genetics and general molecular biological techniques. ATTED-II includes new and updated coexpression data and analysis tools. ATTED-II version 8.0 now includes eight microarray- and six RNAseq-based coexpression data sets for nine species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato, grape, rice and maize). Importantly, five species (Arabidopsis, soybean, tomato, rice and maize) are now supported by both microarray- and RNAseq-based coexpression data.
Provides a genome-scale functional network of Arabidopsis thaliana genes. AraNet can serve to study the functions of genes in Arabidopsis. It is composed of 895 000 linkages among over 22 500 genes. This database includes a collection of co-functional links inferred from diverse genomics data. It enables gene prioritization for non-model plant species, including many food and energy crops.
Gathers a collection of high-quality coexpression data. COXPRESdb concerns highly coexpressed genes, genes with the same gene ontology (GO) annotation, genes expressed in the same tissue and user-defined gene sets. It offers a solution to display and compare the coexpression networks in human and mouse. This platform permits users to discover possible protein-protein interactions (PPIs) effectively.
Presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of CSB.DB is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes.
An internet-based database for plant gene analysis. PLANEX contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization of genes for functional identification and analysis of a gene's dependency among other genes. Gene co-expression databases have been developed for other species, but gene co-expression information for plants is currently limited.
Allows retrieval of summary information about Arabidopsis genes. KAGIANA summarizes various Arabidopsis omics analyses from databases and tools and provides links to pages for genes of interest in databases. The database also provides ‘Tools’ macro programs including ‘Confeito’, ‘GX bar chart’, ‘GO pie chart’ and ‘ATTED chart’. It aims to assist plant biologists in accessing information from omics analyses so that they can incorporate it into their plant biology research.