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NCG / Network of Cancer Genes
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A manually curated repository of cancer genes derived from the scientific literature. NCG release 5.0 (August 2015) collects 1571 cancer genes from 175 published studies that describe 188 mutational screenings of 13,315 cancer samples from 49 cancer types and 24 primary sites. In addition to collecting cancer genes, NCG also provides information on the experimental validation that supports the role of these genes in cancer and annotates their properties (duplicability, evolutionary origin, expression profile, function and interactions with proteins and miRNAs).
Is an improved functional gene network for laboratory mouse, Mus musculus, which is the choice for many biomedical researches. To improve the previous version of MouseNet, a large volume of new microarray data derived from diverse biological contexts has been incorporated. We have also continued to improve machine learning algorithms to infer co-functional links from genomics data. MouseNet v2 now covers 88% of coding genomes with higher accuracy. All of the functional gene networks are released for free and can be searched using the MouseNet v2 web server, which offers a useful resource for mouse, human and other vertebrate genetics.
OrCGDB / Oral Cancer Gene Database
Reports altered genes in oral cancer. OrCGDB is designed to be optimal for utilization of the information for diagnosis, prognosis and treatment. It has been used to predict the possible role of differentially expressed markers in cell transformation. The database provides the scientist information and external links for the genes involved in oral cancer, interactions between them, and their role in the biology of oral cancer along with clinical relevance.
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.
An automatically collected database of gene lists, which were reported mostly by experimental studies in various biological and clinical contexts. At the moment, the database covers 3369 gene lists extracted from 2644 papers published in approximately 80 peer-reviewed journals. As input, CCancer accepts a gene list. An enrichment analyses is implemented to generate, as output, a highly informative survey over recently published studies that report gene lists, which significantly intersect with the query gene list. A report on gene pairs from the input list which were frequently reported together by other biological studies is also provided.
FLOR-ID / Flowering-Interactive Database
An evolutive and interactive database of flowering time genes. The hand-curated database contains information on 306 genes and links to 1595 publications gathering the work of >4500 authors. Gene/protein functions and interactions within the flowering pathways were inferred from the analysis of related publications, included in the database and translated into interactive manually drawn snapshots. The content of the FLOR-ID database could be easily incremented with modules expanding beyond flowering time, for example to gametophyte development.
An accurate and high-resolution atlas of gene expression and gene co-regulation in human retina. We collected 50 high-quality post-mortem human retinas from donors and performed high-coverage RNA-sequencing analysis to yield a comprehensive RefT of the human retina. Moreover, we exploited inter-individual variability in gene expression to infer a gene co-expression network and to predict, via a guilty-by-association approach, photoreceptor-specific expression of 253 genes. This atlas represents a valuable resource for the research community at large and help in better elucidating pathophysiological processes in the human retina.
SorghumFDB / Sorghum functional genomics database
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.
GSKB / Gene Set Knowledgebase
A comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. GSKB is a functional genomics knowledgebase in mouse, which includes 33261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, 8747 lists of differentially expressed genes from 2526 published gene expression studies were manually collected and curated to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute the comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA).
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