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Found 20 result(s)

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

Human Genetic Variation Repository

HGVD

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The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

BioDeep Database

BioDeep Portal

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The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.

MozAtlas

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MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.

mentha

the interactome browser

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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

Genomes OnLine Database

GOLD

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GOLD is currently the largest repository for genome project information world-wide. The accurate and efficient genome project tracking is a vital criterion for launching new genome sequencing projects, and for avoiding significant overlap between various sequencing efforts and centers.

Clinical Genomic Database

CGD

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Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.

PANDIT

Protein and Associated Nucleotide Domains with Inferred Trees

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<<<!!!<<< Efforts to obtain renewed funding after 2008 were unfortunately not successful. PANDIT has therefore been frozen since November 2008, and its data are not updated since September 2005 when version 17.0 was released (corresponding to Pfam 17.0). The existing data and website remain available from these pages, and should remain stable and, we hope, useful. >>>!!!>>> PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.

Genome-Scale Metabolic Network DataBase

GSMNDB

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<<<!!!<<< 2019-12-23: the repository is offline >>>!!!>>> Introduction of genome-scale metabolic network: The completion of genome sequencing and subsequent functional annotation for a great number of species enables the reconstruction of genome-scale metabolic networks. These networks, together with in silico network analysis methods such as the constraint based methods (CBM) and graph theory methods, can provide us systems level understanding of cellular metabolism. Further more, they can be applied to many predictions of real biological application such as: gene essentiality analysis, drug target discovery and metabolic engineering

The Comprehensive Resource of Mammalian protein complexes

CORUM

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CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.

The Taenia solium Genome Project

T. solium Genome Project

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<<<!!!<<< 2021-08; The repository is no longer available. >>>!!!>>> Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

Cotton Functional Genomics Database

CottonFGD

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Cotton Functional Genomics Database (CottonFGD) integrates with modern genomic/transcriptomic data and earch/analysis/visualization modules. It aims at providing an easy, quick and visualized data analysis platform for cotton (Gossypium spp) researchers and other functional genomic researches.

NASC

The European Arabidopsis Stock Centre

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The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to Europe researchers.

Progenetix

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The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32548 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1031 articles and represents 366 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).

NAGRP Blast Center

National Animal Genome Research Program Blast Center

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NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.

arrayMap

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arrayMap is a repository of cancer genome profiling data. Original) from primary repositories (e.g. NCBI GEO, EBI ArrayExpress, TCGA) is re-processed and annotated for metadata. Unique visualization of the processed data allows critical evaluation of data quality and genome information. Structured metadata provides easy access to summary statistics, with a focus on copy number aberrations in cancer entities.

Human Metabolome Database

HMDB

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The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.

National Stem Cell Translational Resource Center

国家干细胞转化资源库

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The National Stem Cell Translational Resource Bank (NSCTRB) contains various stem cell resources of both clinical and research grade, especially a sub-bank composed with HLA high-frequency iPSC lines in which the HLA types could match more than 60% of the Chinese population. It can not only provide services to stem cell clinical researches and translation applications, but also provide effective resources for scientific research to the Universities, research institutes, companies, etc. The bank has complete standards, specifications and relevant management systems, and has more than 200 perfessonals in the field of stem cells.

Wiki-Pi

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Wiki-Pi is a wiki resource centered on human protein-protein interactions. Wiki-Pi's intuitive search functionality allows you to retrieve and discover interactions effectively.

pSILAC

pulsed SILAC

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database of pSILAC data – information about changes in mRNA levels and protein synthesis following microRNA misexpression in HeLa cells