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Found 31 result(s)

BioCyc Genome Database Collection

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The BioCyc database collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes and metabolic pathways of thousands of sequenced organisms. BioCyc PGDBs are generated by software that predict the metabolic pathways of completely sequenced organisms, predict which genes code for missing enzymes in metabolic pathways, and predict operons. BioCyc also integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. From 2016 on, access to the EcoCyc and MetaCyc databases will remain free. Subscriptions to the other 7,600 BioCyc databases will be available to institutions (e.g., libraries), and to individuals. Access to licensed databases via: https://biocyc.org/Product-summary.shtml.

FaceBase

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FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.

Xenbase

Xenopus Genomics Database

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Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.

IMGT/GENE-DB

ImMunoGeneTics / Gene-DB

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IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates. IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps).

Expression Atlas

Gene Expression Atlas

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The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

The Monarch Initiative

Monarch Initiative

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As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.