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Human genome databases | Annotation

The ability to sequence genomes has far exceeded the techniques for deciphering the information they encode. Selecting the correct reference gene annotation for a particular project is extremely important for any downstream analysis such as…
GenBank
Dataset

GenBank

A comprehensive database that contains publicly available nucleotide sequences…

A comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual…

NCBI
Dataset

NCBI National Center for Biotechnology Information

Supplies several online resources for biological information. NCBI is a…

Supplies several online resources for biological information. NCBI is a web-based platform gathering information, tools, and functions that can be useful for researchers about biology. It offers user…

GCGene
Dataset

GCGene Gastric Cancer Gene database

A literature-based database with comprehensive annotations supported by a…

A literature-based database with comprehensive annotations supported by a user-friendly website. In the current release, we have collected 1,815 unique human genes including 1,678 protein-coding and…

IGC
Dataset

IGC integrated gene catalog

Represents a comprehensive resource for further investigations of the gut…

Represents a comprehensive resource for further investigations of the gut microbiome, covering strains with a diverse range of occurrence frequencies. IGC allows rapid and multi-omic profiling of the…

EBI
Dataset

EBI EMBL-EBI - The European Bioinformatics Institute

Supplies an access to several biological data resources. EBI is a database that…

Supplies an access to several biological data resources. EBI is a database that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems,…

CoReCG
Dataset

CoReCG Colon Rectal Cancer Gene Database

Contains 2056 colon-rectal cancer genes information involved in distinct…

Contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system.…

MSGene
Dataset

MSGene Metastasis Suppressor Gene Database

The first literature-based gene resource for exploring human metastasis…

The first literature-based gene resource for exploring human metastasis suppressor genes (MS genes) to unveil the cellular complexity of MS genes. MSGene database stores 194 human MS genes (161…

dbEMT
Dataset

dbEMT

A literature-based gene resource for exploring epithelial-mesenchymal…

A literature-based gene resource for exploring epithelial-mesenchymal transition (EMT)-related human genes. dbEMT includes literature data, clinical relevant variants, gene expression profiles and…

RefSeq
Dataset

RefSeq Reference Sequence

Maintains and curates a publicly available database of annotated genomic,…

Maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records. The RefSeq project leverages the data submitted to the International Nucleotide…

UCSC Genome Browser
Web

UCSC Genome Browser University of California Santa Cruz Genome Browser

Offers online public access to a growing database of genomic sequence and…

Offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The…

BioGPS
Dataset

BioGPS

A centralized gene-annotation portal that enables researchers to access…

A centralized gene-annotation portal that enables researchers to access distributed gene annotation resources. The unique features of BioGPS, compared to those of other gene portals, are its…

Gene
Dataset

Gene

Integrates gene-specific information from multiple data sources. NCBI Reference…

Integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that…

Chromosome 7…
Dataset

Chromosome 7 Annotation Project

Compiles information about chromosome 7. Chromosome 7 Annotation Project…

Compiles information about chromosome 7. Chromosome 7 Annotation Project contains a collation of sequence, gene, and other annotations from databases, such as Celera published, NCBI, Ensembl, RIKEN…

DDBJ
Dataset

DDBJ DNA Data Bank of Japan

Maintains and provides public archival, retrieval and analytical services for…

Maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology…

CCSB-Broad…
Dataset

CCSB-Broad Lentiviral Expression Library

Allows users to search information about genome-scale expression. CCSB-Broad…

Allows users to search information about genome-scale expression. CCSB-Broad Lentiviral Expression Library is a database that provides more than 15 000 human open-reading frames (ORFs). It enables…

hORFeome…
Dataset

hORFeome Database

Provides several informations about single-colony, fully-sequenced cloned…

Provides several informations about single-colony, fully-sequenced cloned human. hORFeome Database consists in genome-scale human ORFeome collections. Users can search: (i) open-reading frames…

CCDS
Dataset

CCDS Consensus Coding Sequence

A collaborative effort to maintain a dataset of protein-coding regions that are…

A collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology…

GeneMap
Dataset

GeneMap

Unifies the existing genetic and physical maps with the nucleotide and protein…

Unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The GeneMap…

HipSci
Dataset

HipSci human induced pluripotent Stem cells initiative

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy…

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy individuals as well as patients diagnosed with selected diseases. HipSci is a powerful resource to evaluate and…

Gene Wiki
Dataset

Gene Wiki

Gathers Wikipedia articles about human genes. Gene Wiki aims to constitute a…

Gathers Wikipedia articles about human genes. Gene Wiki aims to constitute a continuously updated, community-reviewed and collaboratively written review article for every human gene. The database…

Metascape
Web

Metascape

A web portal for gene annotation and analysis resource that helps biologists…

A web portal for gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists. Metascape provides automated meta-analysis tool to understand common and unique…

H-InvDB
Dataset

H-InvDB

Provides useful data mining resources, an enrichment analysis tool and web…

Provides useful data mining resources, an enrichment analysis tool and web service APIs. H-InvDB is a comprehensive annotation resource of human genes and transcripts. This database includes gene…

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HGPD
Dataset

HGPD Human Gene and Protein Database

Compiles a set of protein expression and protein synthesis data added to human…

Compiles a set of protein expression and protein synthesis data added to human Gateway entry clones. HGPD compiles more than 40000 entry clones splitted in 10 protein function groups. The database…

Repositive
Dataset

Repositive

Enables researchers to browse through multiple repositories for the human…

Enables researchers to browse through multiple repositories for the human genomic data they need to power their research. Repositive includes features for discovery of available data, making data…

G T A T C G C T A
Highlander
Desktop

Highlander

A Java software coupled to a local database to centralize all variant data and…

A Java software coupled to a local database to centralize all variant data and annotations from the lab, and to provide powerful filtering tools that are easily accessible to the biologist. Data can…

BIG Data Center
Dataset

BIG Data Center

A data repository for constructing and maintaining biological databases to aid…

A data repository for constructing and maintaining biological databases to aid translation of big data into big discover. The BIG Data Center takes full advantages of valuable resources and…

PEDANT
Dataset

PEDANT

Provides exhaustive automatic analysis of genomic sequences by a large variety…

Provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools. PEDANT is a database that includes (i) integration with the BioRSTM data retrieval system which…

PCOSKB
Dataset

PCOSKB

A manually curated knowledgebase on polycystic ovary syndrome (PCOS).…

A manually curated knowledgebase on polycystic ovary syndrome (PCOS). PCOS-related information available through scientific literature is cross-linked with molecular, biochemical and clinical…

HGNC
Dataset

HGNC HUGO Gene Nomenclature Committee

Provides a unified nomenclature for all genes of the human genome. HGNC…

Provides a unified nomenclature for all genes of the human genome. HGNC supplies a manually curated base created in collaboration with researchers specialized on particular fields. A public access…

DREMECELS
Dataset

DREMECELS DNA REpair MEchanism in Colorectal Endometrium and Lynch Syndrome

A curated database for base excision and mismatch repair mechanisms associated…

A curated database for base excision and mismatch repair mechanisms associated human malignancies. DREMECELS contains 156 genes and two repair mechanisms, base excision repair (BER) and mismatch…

HEROD
Dataset

HEROD Human Ethnic and Regional specific Omics Database

Focuses on the collection of the most comprehensive sets of gene expression…

Focuses on the collection of the most comprehensive sets of gene expression data with available personal traits information. HEROD offers 14 different search modes. It contains more than 53 000…

IDBD
Dataset

IDBD Infectious Disease Biomarker Database

Catalogs putative and validated biomarkers and relates them to infectious…

Catalogs putative and validated biomarkers and relates them to infectious diseases processes. IDBD was designed to collect, store and display information about biomarkers, conjoined to research tools…

RAAR
Dataset

RAAR Regulators of Androgen Action Resource

A web-based user-friendly searchable database to study androgen action in…

A web-based user-friendly searchable database to study androgen action in prostate cancer more efficiently. RAAR centralizes information on gene function, clinical relevance, and resources for the…

AlzBase
Dataset

AlzBase

An integrative database for gene dysregulation in Alzheimer's disease.…

An integrative database for gene dysregulation in Alzheimer's disease. AlzBase collects several categories of information, including (1) gene dysregulation in AD and closely related…

IGRhCellID
Dataset

IGRhCellID Integrated Genomic Resources of Human Cell Lines for Identification

Collects genomic resources of common human cell lines. IGRhCellID provides…

Collects genomic resources of common human cell lines. IGRhCellID provides short tandem repeat (STR) profiles of human cell lines and tools with conventional laboratory polymerase chain reaction…

NCBI Genome
Dataset

NCBI Genome

This resource organizes information on genomes including sequences, maps,…

This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.

MuGI
Desktop

MuGI Multiple Genome Index

A compressed index of collections of genomes of the same species. MuGI reports…

A compressed index of collections of genomes of the same species. MuGI reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s)…

GENCODE
Dataset

GENCODE

Aims to identify all gene features in the human genome using a combination of…

Aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation…

KEGG GENES
Dataset

KEGG GENES

Provides a collection of completely sequenced genomes. KEGG GENES contains gene…

Provides a collection of completely sequenced genomes. KEGG GENES contains gene catalogs mainly generated from NCBI RefSeq and GenBank. The database is enriched with a set of metagenome data and…

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OmicsDI
Dataset

OmicsDI Omics Discovery Index

Permits to access, discover and disseminate omics data sets. OmicsDI is an…

Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform…

CaGeDb
Dataset

CaGeDb Calcium Gene Database

Stores genes connected to calcium signaling and their associated diseases.…

Stores genes connected to calcium signaling and their associated diseases. CaGeDb is an online database, built using Gene Ontology (GO) terms and genome databases, which provides a map of all of the…

euGenes
Dataset

euGenes

A genome information system and database that provides a common summary of…

A genome information system and database that provides a common summary of eukaryote genes and genomes.

EVOG
Dataset

EVOG Evolution Visualizer for Overlapping Genes

An integrated database for overlapping genes that includes bioinformatics…

An integrated database for overlapping genes that includes bioinformatics analysis data. EvOG supports all overlapping genes that are common in a subset of Human, Chimpanzee, Orangutan, Marmoset,…

SEGEL
Dataset

SEGEL Smoking Effects on Gene Expression of Lung

An online web server for easy and fast visualization of smoking effects on…

An online web server for easy and fast visualization of smoking effects on human lung gene expression. SEGEL integrates 362 samples collected from eight public expression microarray data sets from…

Harmonizome
Dataset

Harmonizome

A collection of processed datasets gathered to serve and mine knowledge about…

A collection of processed datasets gathered to serve and mine knowledge about genes and proteins from over 70 major online resources. We extracted, abstracted and organized data into approximately 72…

REGene
Dataset

REGene REgeneration Gene database

A literature-based gene resource dedicated to furthering animal research by…

A literature-based gene resource dedicated to furthering animal research by integrating multi-dimensional bioinformatics data. REGene contains 948 human (929 protein-coding and 19 non-coding genes)…

BGDB
Dataset

BGDB

Provides several types of information about genomic data, sequences, or gene…

Provides several types of information about genomic data, sequences, or gene ontology (GO). BGDB is a literature-based resource of bivalent genes that assists users to better understand the mechanism…

NGD
Dataset

NGD Nencki Genomics Database

Extends the functionality of Ensembl Regulatory Build for the three species:…

Extends the functionality of Ensembl Regulatory Build for the three species: human, mouse and rat. NGD is a database containing information on conserved non-coding sequences and on genome-wide…

OKdb
Dataset

OKdb Ovarian Kaleidoscope Database

Provides information regarding the biological function, expression pattern and…

Provides information regarding the biological function, expression pattern and regulation of genes expressed in the ovary. OKdb also contains information on gene sequences, chromosomal localization,…

hLGDB
Dataset

hLGDB The Human lysosome Gene Database

Focuses on the census of genes belonging to the lysosomal system and on their…

Focuses on the census of genes belonging to the lysosomal system and on their regulation by microRNAs (miRNAs). hLGDB collects information about human lysosomal genes and their transcriptional…

HTD
Dataset

HTD Human Transporter Database

A comprehensive gene resource for human transporters. We also collect the…

A comprehensive gene resource for human transporters. We also collect the information of the mouse and rat transporters for reference.

OC
Dataset

OC ORFeome Collaboration

Represents a resource about genome-scale clone for human genes. The collection…

Represents a resource about genome-scale clone for human genes. The collection of OC contains open reading frame (ORF) clones and covers more than: (1) 17000 RefSeq and Ensembl genes, (2) 70% of…

simulatorZ
Desktop

simulatorZ

Simulates collections of independent genomic data sets, and performs training…

Simulates collections of independent genomic data sets, and performs training and validation with predicting algorithms. SimulatorZ is a package intended primarily to simulate collections of…

Pedican
Dataset

Pedican Pediatric cancer gene database

A database committed to establishing a comprehensive gene resource for…

A database committed to establishing a comprehensive gene resource for pediatric/childhood cancer by comprehensive literature curation and data integration. Pedican includes literature data, clinical…

GPA
Dataset

GPA Gene Perturbation Atlas

A database that includes a comprehensive collection of transcriptome profiles…

A database that includes a comprehensive collection of transcriptome profiles of protein coding genes, miRNAs and lncRNAs perturbed by knockdown or overexpression in human and mouse. GPA offers a…

CGMD
Dataset

CGMD Cancer Gene Marker Database

A database which integrates data on tumor genes and markers based on…

A database which integrates data on tumor genes and markers based on experimental evidence. The major goal of CGMD is to provide the following: 1) current systematic treatment approaches and recent…

AceDB
Dataset

AceDB A C. elegans DataBase

Provides a custom database kernel, with a non-standard data model designed…

Provides a custom database kernel, with a non-standard data model designed specifically for handling scientific data flexibly, and a graphical user interface with many specific displays and tools for…

eGOB
Web

eGOB eukaryotic Gene Order Browser

Views any eukaryotic gene and its genomic environment in different species.…

Views any eukaryotic gene and its genomic environment in different species. eGOB is an online tool that offers informations on the order of protein and non-coding RNA (ncRNA) genes of 74 different…

HNOCDB
Dataset

HNOCDB Head Neck and Oral Cancer DataBase

Provides essential information for researchers working on head and neck and…

Provides essential information for researchers working on head and neck and oral cancer (HNOC). HNOCDB serves as a ‘crossroad/junction’ database, where information regarding a particular…

IntegromeDB
Dataset

IntegromeDB

A biological web search engine based on the Semantic Web technologies. The…

A biological web search engine based on the Semantic Web technologies. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways,…

HelmCoP
Dataset

HelmCoP Helminth Control and Prevention

An online resource built by integrating functional, structural and comparative…

An online resource built by integrating functional, structural and comparative genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and…

VeryGene
Dataset

VeryGene

A curated, web-accessible centralized database for the annotation of…

A curated, web-accessible centralized database for the annotation of tissue-specific/enriched genes. VeryGene currently contains entries for 3960 human genes covering 128 normal tissue/cell types…

TuMa Rdb
Dataset

TuMa Rdb Tumor Markers Reference database

Gathers tumor marker references in several diseases.

Gathers tumor marker references in several diseases.

iGenomes
Dataset

iGenomes

Provides a set of reference sequences and annotation files for common…

Provides a set of reference sequences and annotation files for common organisms. iGenomes has been constructed with data from Ensembl, NCBI and UCSC. Chromosome names have been simplified to be…

gnomAD
Dataset

gnomAD Genome Aggregation Database

Aggregates and harmonizes exome and genome sequencing data from a variety of…

Aggregates and harmonizes exome and genome sequencing data from a variety of large-scale sequencing projects, and makes summary data available for the wider scientific community. The gnomAD data set…

PCGP
Web
Desktop

PCGP Pediatric Cancer Genome Project

Facilitates access to high-quality genomic data for pediatric cancers. PCGP is…

Facilitates access to high-quality genomic data for pediatric cancers. PCGP is a webserver which aims to accelerate discovery and hypothesis testing, to provide comprehensive visualizations of the…

CloneCollection
Dataset

CloneCollection

Contains a collection of statistics concerning: kinases, cell death, membrane…

Contains a collection of statistics concerning: kinases, cell death, membrane proteins, nuclear proteins, metabolism, signal transduction, secreted proteins, and transcription factors.…

GeneCards
Dataset

GeneCards

A searchable, integrative database that provides comprehensive, user-friendly…

A searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web…

CancerGenes
Dataset

CancerGenes

Enables gene list storage, queries and comparisons. CancerGenes aims to…

Enables gene list storage, queries and comparisons. CancerGenes aims to simplify gene selection process in resequencing projects, especially in large, geographically dispersed, collaborative groups.…

Integr8
Dataset

Integr8

Offers interactive access to data integrated from Genome Reviews and other…

Offers interactive access to data integrated from Genome Reviews and other resources, centred around organisms with completely sequenced genomes. Integr8 contains statistical analyses of those…

ERGR
Dataset

ERGR Ethanol-Related Gene Resource

Gathers information about ethanol-related gene. ERGR is a database of…

Gathers information about ethanol-related gene. ERGR is a database of ethanol-related gene resource allowing to analyze a lot of the published ethanol-related gene studies. In this platform, the…

SesameFG
Dataset

SesameFG Sesame Functional Genomics Database

Promotes sesame functional genomics research. SesameFG is an integrated…

Promotes sesame functional genomics research. SesameFG is an integrated repository of comprehensive genotype-phenotype information that provides comprehensive genetic information, phenotypic…

GuavaH
Dataset

GuavaH Genomic Utility for Association and Viral Analyses in HIV

Provides results from genome-wide association (GWAS) of human immunodeficiency…

Provides results from genome-wide association (GWAS) of human immunodeficiency virus (HIV) disease phenotypes including more than 4,000 individuals. GuavaH includes association results on HIV control…

WikiGenomes
Dataset

WikiGenomes

Facilitates the consumption and curation of genomic data by the entire…

Facilitates the consumption and curation of genomic data by the entire scientific community. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation…

DBGC
Dataset

DBGC Database of Human Gastric Cancer

A comprehensive database that integrates various human gastric cancer-related…

A comprehensive database that integrates various human gastric cancer-related data resources. DBGC collects and unifies Human gastric cancer-related transcriptomics projects, proteomics projects,…

RefGene
Dataset

RefGene

Contains information about human and non-human genes and antibodies. RefGene is…

Contains information about human and non-human genes and antibodies. RefGene is a database, implemented as a web user interface, which provides information on genes, such as a summary, orthologs and…

HostDB
Dataset

HostDB

An integrated genomic and functional genomic database for interrogation of host…

An integrated genomic and functional genomic database for interrogation of host responses to infection. HostDB supports host data obtained during infections by organisms supported by EuPathDB's…

ReCGiP
Dataset

ReCGiP

A database providing candidate genes for reproductive researches in pig by…

A database providing candidate genes for reproductive researches in pig by mining and processing existing biological literatures in human and pigs. Based on text-mining and comparative genomics,…

PRIME
Dataset

PRIME PRotein Interactions and Molecular Information databasE

An integrated gene/protein informatics database based on natural language…

An integrated gene/protein informatics database based on natural language processing. PRIME provides automatically extracted protein/family/gene/compound interaction information including both…

Information

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