Tag: human

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all ...

The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more ...

The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored w ...

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-co ...

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications i ...

PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to ...

ProteomicsDB is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of ...

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In ke ...

The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is e ...

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Databas ...

Overview The NIH Mammalian Gene Collection (MGC) program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse, and rat genes. To date, the MGC has produced over 324 ...

VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...

The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. The IHEC Data Portal pr ...

IMGT/GENE-DB is the IMGT® comprehensive genome database for immunoglobulins (IG) and T cell receptors (TR) genes from human and mouse, and, in developement, from other vertebrate species (e.g. rat). IMGT/GENE-DB is part of IMGT®, the international ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

dbSTS is an NCBI resource that contains sequence data for short genomic landmark sequences or Sequence Tagged Sites.

Analysis of finished and draft mouse genomic clone sequences.

Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).

This ensembl website features the zebrafish whole genome shotgun assembly sequence.

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).

Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.

Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl's comparative genomics resources.

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

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 variation ...

The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.

Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. ...

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 ...

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

The objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

dbSUPER is the first integrated and interactive database of super-enhancers, which contains 82234 super-enhancers in 102 human and 25 mouse tissue/cell types.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.

Gene expression data sorted into two groups: expressed and not expressed genes

CLIMA 2 is the result of an integration effort aimed at including all certified STR profiles of human cell lines in a unique database. The contents of the database are dynamically summarized (i.e., they are always up-to-date) in a table in the home p ...

Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

The Integrated Interactions Database (IID) is a database of detected and predicted protein-protein interactions (PPIs) in a number of species. It stores networks that are specific to tissues, sub-cellular localizations, diseases, and druggable protei ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

PGG.SNV is database for understanding the evolutionary and medical implications of human single nucleotide variation (SNV) on a population level. It documents more than 300,000 genomes and 10 billion allele frequencies records for diverse human ethni ...

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

Analyzing curated annotations to associate animal models with human diseases.

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq p ...

Blood Group Antigen Gene Mutation Database

Essential gene profiles in human cancer cell lines

Association of human lncRNAs with disease-related SNPs

GenAtlas is a database containing information on human genes, markers and phenotypes.

HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).

Polymorphic inversions in the human genome

Curated compendium of specific DNA-binding RNA polymerase II transcription factors.

Attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

PICKLE (Protein InteraCtion KnowLedgebasE) is a meta-database for the direct protein-protein interactome of the human and the mouse proteomes, integrating publicly available source protein-protein interaction (PPI) databases via genetic information o ...

Polyglutamine Repeats in Proteins

Reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.

Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available.

Structural Atlas of Human Genome

A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific commu ...

Database of molecular-level putative protein-drug interactions in the structural human proteome.

Collaboration between the astronomers, laboratory chemists and theoretical chemists at the facilities of NASA's Ames Research Center resulted in the collection of PAH spectra known as The NASA Ames PAH IR Spectroscopic Database. Collaboration with di ...

An online gene resource for pediatric cancers with literature evidence.

an annotated database of protein associations. Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE.These associations represent a broad scala of biological a ...

GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces ar ...

A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue.

A resource of human disease associated mutations from next generation sequencing studies.

The human Ensemble Cell Atlas (hECA) a database.

User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

A mesocosm database management system for environmental nanosafety.

A repository for collection and distribution of plasmid clones

PrimateDatabase.com, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology. PrimateDatabase.com is unique because it is currently the l ...

Gene annotation portal and a resource on gene and protein function

Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom ...

Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cy ...

Collection of samples and data across the following diseases: Complete trisomy 21 syndrome (disorder) The HBRC is an HTA-licensed biorepository dedicated to the collection of appropriately consented high quality human biomaterials, their processing, ...

Collection of samples and data across the following diseases: Entire embryo (body structure) The Human Developmental Biology Resource (HDBR) is an ongoing collection of human embryonic and fatal material ranging from 3 to 20 weeks of development. Mat ...

HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature.

A comprehensive database for human proteome repeats. Human Proteome Repeats Database. HPREP : HUMAN PROTEOME REPEATS.

Exposome of Human Milk across India (ExHuMId) is a curated resource and analysis of exposome of human milk across India.

Database of human autophagy modulators with specific pathway and disease information.

An integrative platform to navigate the biology, structure and chemical inhibition of human proteins.

ETph is a database for enhancer and their targets in pig and human.

QSHGM, a database of QS in Human Gut Microbiota includes 28,567 redundancy removal QS synthases and receptors entries of 818 gut microbes.

A functional human brain atlas termed D-BFA (DFC-based Brain Functional Atlas)

The (Zebrafish) Xenograft Phenotype Interactive Repository (Xe.Ph.I.R) is an online database for describing how human cancer behaves when engrafted in zebrafish embryos. We provide representative images of the first days of cancer development post-en ...

Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a grap ...

A Cross-sectional Analysis of the US Food and Drug Administration Manufacturer and User Facility Device Experience Database.

We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in i ...

NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering ...

Alzforum is an independent research project to develop an online community resource to manage scientific knowledge, information, and data about Alzheimer disease (AD).

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. We study diseases that have an impact on health globally by investigating genomes. Building on our past a ...

!!! >>> intrepidbio.com expired <<< !!!! Intrepid Bioinformatics serves as a community for genetic researchers and scientific programmers who need to achieve meaningful use of their genetic research data – but can’t spend tremendous amounts of time ...

The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northweste ...

>>> !!! the repository is offline !!! <<< More information see: https://dknet.org/about/NURSA_Archive All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine ...

<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome ...

!!! >>> The repository is offline <<< !!! One of the world’s largest banks of biological, psychosocial and clinical data on people suffering from mental health problems. The Signature center systematically collects biological, psychosocial and clinic ...

>>>!!! NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post. Links to Clone DB from the NCBI home page ...

ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, spl ...