A probabilistic functional gene network for baker's yeast, Saccharomyces cerevisiae, which has been a major model organism for eukaryotic genetics and cell biology. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (approximately 2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links.
Provides a brain-specific functional gene network. BaiHui is an online resource that allows users to query networks of their genes of interest, visualize the resulting local networks, gain functional insight from enrichment analysis and download network data. It can be used to generate hypotheses about disease candidate genes of brain disorders including Parkinson’s disease (PD) and Alzheimer’s disease (AD).
A platform for genome functional annotations and multi-dimensional network analyses in Sorghum (Sorghum bicolor [L.] Moench). SorghumFDB encompassed most information, such as various annotations of whole genome assemblies, miRNA sequences and target genes, common gene families, network constructions using transcriptome data, PPI data and miRNA-target pairs, as well as multiple gene function annotation elements. Visualization tools (Gbrowse, Cytoscape and open-flash-chart) and four analysis-based tools, BLAST, GSEA, motif significance analysis and pattern set, were provided to determine the functional prediction.
A database of cancer gene networks estimated from the publicly available cancer gene expression data. TCNG allows to estimate genome-wide gene networks consisting of more 20,000 genes from gene expression data using nonparametric Bayesian networks. The gene networks are estimated using the Japanese national flagship supercomputer "K computer". This is a result of ISLiM project which aims at developing biological software that utilizes "K computer".
Compiles information related to biological relationships. iBioGuide provides a repository of networks gathered by the Advaita company. This platform supplies a free-text search engine allowing queries by gene, pathway, miRNAs, gene ontology or diseases, where data can be filtered by organisms. Result page displays advanced information about a gene and its corresponding literature as well as panels allowing users to see which biological processes, molecular functions, cellular components, miRNAs, pathways, drugs or diseases can be linked to a given gene.
A probabilistic functional gene network for Escherichia coli, which is an intensively studied species of bacteria, due to its utility in both exploring the molecular mechanisms underlying fundamental biological processes and manufacturing useful metabolites for the biomedical industry. All integrated cofunctional associations can be downloaded, enabling orthology-based reconstruction of gene networks for other bacterial species as well.
Provides a manually curated repository of cancer genes derived from scientific literature. NCG collects more than 2300 genes whose somatic modification is known or predicted to possess a cancer driver role. Users can annotate the systems-level properties such as evolutionary origin, duplicability, RNA/protein and miRNA/protein interactions. It serves for the study of individual genes and characterization of cancer genes as a group.