Tag: gene expression


Found 335 sources
Source Match ReputationScore*

Gene Ontology


The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...
100%

UniProt Knowledgebase


Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...
91%

UCSC Genome Browser database


Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.
79%

Gene Expression Omnibus


The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to dat ...
77%

Human Protein Atlas


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 ...
71%

Investigation Study Assay Tabular


General-purpose ISA-Tab file format - an extensible, hierarchical structure that focuses on the description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships).
63%

Comparative Toxicogenomics Database


Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...
57%

Minimum Information for Publication of Quantitative Real-Time PCR Experiments


The aim of MIQE, coordinated by a group of research-active scientists, is to provide authors, reviewers and editors specifications for the minimum information that must be reported for a qPCR experiment in order to ensure its relevance, accuracy, cor ...
56%

Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource


MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homo ...
55%

Minimum Information About a Microarray Experiment


MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.
55%

ArrayExpress


ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...
53%

FlyBase


Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...
52%

The UCSC Archaeal Genome Browser


The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...
52%

Database of Genotypes and Phenotypes


The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.
51%

Saccharomyces Genome Database


The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
50%

Influenza Research Database


The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...
49%

WormBase


WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...
48%

TRANSFAC


Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.
47%

Ensembl Genomes


The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...
47%

BioModels


BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...
47%

The Zebrafish Information Network


The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...
47%

Expression Atlas


The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...
46%

The Arabidopsis Information Resource


The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
46%

doRiNA


Database of RNA interactions in post-transcriptional regulation.
46%

NIDDK Information Network


The NIDDK Information Network provides access to large pools of data relevant to the mission of NIDDK. The dkNET portal contains information about research resources such as antibodies, vectors and mouse strains, data, protocols, and literature.
46%

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants


Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...
45%

Pharmacogenomics Knowledge Base


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 ...
45%

VectorBase


VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contain ...
44%

Virus Pathogen Database and Analysis Resource


The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...
44%

Mouse Phenome Database


Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...
44%

NONCODE


NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...
44%

ExPASy Bioinformatics Resource Portal


Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...
43%

ABA Adult Mouse Brain


ABA Adult Mouse Brain is a standardised collection of the expression patterns of thousands of adult brain genes. This resource can be used for a vast array of research on brain organisation and function. There are lighter versions of this ontology th ...
43%

Xenopus laevis and tropicalis biology and genomics resource


Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the li ...
43%

GTEx


Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.
42%

ENCODE Project


The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...
42%

ViralZone


ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.
41%

PCR Primer Database for Gene Expression Detection and Quantification


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 ...
41%

PomBase


PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...
41%

GenePattern GeneSet Table Format


GenePattern GeneSet Table Format is an analytical tool and file format for the analysis of gene expression and network analysis provided by GenePattern.
41%

Database of genomic structural VARiation


dbVar is a database of genomic structural variation. It accepts data from all species and includes clinical data. It can accept diverse types of events, including inversions, insertions and translocations. Additionally, both germline and somatic vari ...
41%

Expressed Sequence Tags database


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 ...
40%

The Autism Chromosome Rearrangement Database


The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data.
40%

Plant Transcription Factor Database


Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 5 ...
40%

Functional ANnoTation Of the Mammalian genome Database


FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.
40%

TDR Targets


Identification and ranking of targets and bioactive compounds against neglected tropical diseases. TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and che ...
39%

EcoCyc E. coli Database


EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...
39%

Gene Ontology (GO) Gene Association File Format 2.1


Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...
39%

UniGene gene-oriented nucleotide sequence clusters


Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
39%

arrayMap - Genome Profiles in Cancer


The arrayMap database and bioinformatics resource facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by ...
38%

miRTarBase


As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to fu ...
38%

CRISPRFinder


Detects this family of direct repeats found in the DNA of many bacteria and archaea.
38%

Yeast Searching for Transcriptional Regulators and Consensus Tracking


YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...
38%

Maize Genetics and Genomics Database


MaizeGDB is the maize research community's central repository for genetics and genomics information.
38%

Mammalian Gene Collection


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 ...
38%

Progenetix - genomic copy number aberrations in cancer


The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...
37%

PLEXdb


PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...
37%

NCBI BioSample


The BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials used in experimental assays, from which data stored in NCBI’s primary data archives are derived.
37%

NCBI Probe Database


The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
37%

Interferome


This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...
37%

RegulonDB


RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...
37%

DataBase of Transcriptional Start Sites


This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.
37%

H-Invitational Database


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 ...
37%

Gene Ontology (GO) Gene Association File Format 2.2


Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.2 (GAF 2.2). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...
36%

Plant Ontology


The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plant ...
36%

Arabidopsis Information Portal


The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...
36%

e-Mouse Atlas


The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which informatio ...
36%

Cellosaurus


The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines w ...
36%

Giga Science Database


GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e. ...
36%

Genetic and Genomic Information System


GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...
36%

Animal Transcription Factor Database


AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...
36%

Chemical Effects in Biological Systems (CEBS)


CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data d ...
36%

IMGT/GENE-DB


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 ...
36%

Open Regulatory Annotation


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 ...
36%

Princeton University MicroArray database


The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.
36%

e-Mouse Atlas of Gene Expression


EMAGE is a database of in situ gene expression data in the mouse embryo. mRNA in situ hybridisation, protein immunohistochemistry, in situ transgenic reporter data, and in situ enhancer data is included. These are sourced from the community and curat ...
35%

Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments


MISFISHIE is the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments. This specification details the minimum information that should be provided when publishing, making public, or exchanging results from v ...
35%

Online GEne Essentiality database


Online GEne Essentiality database
35%

GWIPS-viz


GWIPS-viz is a freely available on-line genome browser which provides pre-populated ribosome profiling (Ribo-seq) and mRNA-seq tracks from published studies.
35%

MGI Mouse Gene Expression Database


The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for compre ...
35%

zfishbook


Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.
35%

BioCyc


The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, p ...
34%

BIG Data Center


The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...
34%

Regulatory Element Database for Drosophila


REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence ...
34%

canSAR


canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.
34%

BloodSpot


BloodSpot is a database of mRNA expression in healthy and malignant haematopoiesis and includes data from both humans and mice. The core function of BloodSpot is to provide an expression plot of genes in healthy and cancerous haematopoietic cells at ...
34%

Animal Quantitative Trait Loci (QTL) Database


The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...
34%

Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system


Open TG-GATEs is a public toxicogenomics database developed so that a wider community of researchers could utilize the fruits of TGP and TGP2 research. This database provides public access to data on 170 of the compounds catalogued in TG-GATEs. Data ...
34%

AmoebaDB


AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...
34%

Fly-FISH


Fly-FISH documents the expression and localization patterns of Drosophila mRNAs at the cellular and subcellular level during early embryogenesis and third instar larval tissues. A high-resolution, high-throughput fluorescence detection method is used ...
34%

Codon Usage Database


Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
34%

Arabidopsis Thaliana Trans-factor and cis-Element prediction Database


ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...
34%

lncRNAdb


Long Non-Coding RNA Database
34%

Allen Brain Atlas


Gene expression and neuroanatomical data.
34%

Library of Integrated Network-Based Cellular Signatures Data Portal


The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...
33%

AgBase


AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
33%

YeastMine


Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.
33%

Pancreatic Expression database


The Pancreatic Expression Database (PED) is a repository for pancreatic-derived -omics data. With a generic web-based system, the database provides the research community with an open access tool to mine currently available pancreatic cancer experime ...
33%

MicrobesOnline


A suite of Web-based tools for comparative genomics
33%

Drosophila gross anatomy


A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annot ...
33%

Database of Arabidopsis Transcription Factors


The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...
33%

Minimum Information About a Microarray Experiment involving Plants


MIAME/Plant is a standard describing which biological details should be captured for describing microarray experiments involving plants. Detailed information is required about biological aspects such as growth conditions, harvesting time or harvested ...
33%

The Arabidopsis Gene Regulatory Information Server


The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...
33%

Gemma


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. ...
33%

LncBook


LncBook is a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. It integrates multi-omics ...
33%

Network of Cancer Genes


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 ...
32%

A Systematic Annotation Package


ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they mo ...
32%

The Chromosome 7 Annotation Project


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.
32%

TransmiR


TransmiR is a database for transcription factor-microRNA regulations, which is free for academic usage.
32%

PlnTFDB


The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...
32%

Nottingham Arabidopsis Stock Centre Seeds Database


The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
32%

Bgee DataBase for Gene Expression Evolution


Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expr ...
32%

PAZAR


PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...
32%

Minimum Information About a RNAi Experiment


Minimum Information About an RNAi Experiment (MIARE) is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. MI ...
32%

ThaleMine


ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.
32%

ViBE-Z: The Virtual Brain Explorer for Zebrafish


ViBE-Z, the Virtual Brain Explorer for Zebrafish is an imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with prec ...
32%

miRNEST


miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...
32%

Ascidian Network for In Situ Expression and Embryological Data


Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...
32%

Online Mendelian Inheritance in Animals


Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).
32%

SOURCE


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 ...
32%

Signaling Pathway Integrated Knowledge Engine


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 ...
32%

PrognoScan


Database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between ge ...
32%

LINCS Extended Metadata Standard: Differentiated Cells


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Primary Cells


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Cell lines


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Proteins


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Induced Pluripotent Stem Cells


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Other Reagents


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Small molecules


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

LINCS Extended Metadata Standard: Antibody Reagents


LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...
32%

Minimum Information about an ENVironmental transcriptomic experiment


MIAME defines a conceptual structure for defining the core information that is common to most microarray experiments. MIAME/Env is an extension of these guidelines to cover environmental genomics.
32%

Database of Genomic Variants archive (DGVa)


The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...
31%

CleanEx


CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-datas ...
31%

Human Gene and Protein Database


Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.
31%

GeneNetwork


GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...
31%

RTPrimerDB


RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisa ...
31%

PROkariotIC Database Of Gene-Regulation


PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.
31%

DIANA-miRGen


Provides accurate cell-line-specific miRNA gene transcription start sites, coupled with genome-wide maps of transcription factor binding sites in order to unveil the mechanisms of miRNA transcription regulation. The database schema and web interface ...
31%

RegPrecise


Predicted regulons in prokaryotic genomes
31%

Tomato Functional Genomics Database


The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.
31%

Newt-omics


A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive ann ...
31%

GeneSigDB


Gene Signature DataBase
31%

Nematode.net


Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...
31%

HymenopteraMine


HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.
31%

ProPortal


ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organization—from the genome to ...
31%

SAGEmap


SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...
31%

FlyFactorSurvey


Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
31%

Affymetrix NetAffx Analysis Center


Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.
31%

The Improved Database Of Chimeric Transcripts and RNA-Seq Data


The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...
31%

mirEX


mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.
31%

Generic Feature Format Version 3


The Generic Feature Format Version 3 (GFF3) format was developed after earlier formats, although widely used, became fragmented into multiple incompatible dialects. The GFF3 format addresses the most common extensions to GFF, while preserving backwar ...
31%

Bovine Genome Database


The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.
30%

MutDB


The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...
30%

Type 1 Diabetes Database


T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.
30%

DroID - Drosophila Interactions Database


DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...
30%

RiceXPro


Rice transcriptome under natural conditions
30%

Transcription Factor Class Schema


The TFClass Schema is an identifier schema for classifying transcription factors according to a six-level schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene ...
30%

Gene Expression Barcode


Gene expression data sorted into two groups: expressed and not expressed genes
30%

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures


Gene Signature DataBase (GeneSigDB) is a database of gene signatures (or gene sets) that have been extracted and manually curated from articles that are indexed by PubMed.
30%

Database of small human non-coding RNAs


Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs.
30%

Japanese Genotype-phenotype Archive


The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects.
30%

Integrated Tumor Transcriptome Array and Clinical data Analysis database


ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular ...
30%

EpiFactors


EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...
30%

LegumeIP


The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes.
30%

Saccharomyces cerevisiae Transcription Factor Database


ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...
30%

Transcription Factor Class


TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phyloge ...
30%

Database of Rice Transcription Factors


DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF incl ...
30%

CLIPZ


Experimentally-determined binding sites of RNA-binding proteins
30%

SilkDB


The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...
30%

GeneProf


GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public ...
30%

CellFinder


CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells ...
30%

Virtual Fly Brain


VFB is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagent ...
30%

ChimerDB


ChimerDB is a database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data and integration with other well known databases. Fusion transcripts with nonoverlapping ali ...
30%

Geneimprint


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.
30%

SubtiWiki


Collaborative resource for the Bacillus community.
30%

Plant Natural Antisense Transcripts Database


Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform fo ...
29%

FaceBase


FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...
29%

Plant MicroRNA Database (PMRD)


The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and ...
29%

MouseMine @ MGI


A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system ...
29%

BioXpress


BioXpress is a curated gene expression and disease association database where the expression levels are mapped to genes.
29%

The Database of Human DNA Methylation and Cancer


The database of human DNA Methylation and Cancer (MethyCancer) is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer informati ...
29%

Mouse Atlas of Gene Expression


The Mouse Atlas of Gene Expression is a quantitative and comprehensive atlas of gene expression in mouse development. Gene expression levels from 198 tissue samples was measured using 202 Serial Analysis of Gene Expression (SAGE). Emphasis was on mou ...
29%

Database of Differentially Expressed Proteins in Human Cancer


The dbDEPC is a database of differentially expressed proteins in human cancers.
29%

CIBEX


Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.
29%

Drosophila DNase I footprint database


Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
29%

StellaBase


StellaBase is the Nematostella vectensis genomics database.
29%

MERAV


Metabolic gEne RApid Visualizer
29%

FGDB


Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the ...
29%

Kidney and Urinary Pathway Knowledgebase


The KUPKB is a collection of omics datasets that have been extracted from scientific publications and other related renal databases. The iKUP browser provides a single point of entry for you to query and browse these datasets.
28%

Neural-Immune Gene Ontology


The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to ...
28%

Integrated Genomic Database of Non-Small Cell Lung Cancer


Integrated Genomic Database of Non-Small Cell Lung Cancer.
28%

Multi Experiment Matrix (MEM)


MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global orderin ...
28%

Genomic Expression Archive


Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and ...
28%

expVIP


Customizable RNA-seq Data Analysis and Visualization Platform.
28%

EchoBase


EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.
28%

WebGeSTer DB


WebGesTer Database (DB) is the largest compilation of intrinsic terminators of transcription. It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. The database is the storehouse for algorithm ...
28%

FlyTF


FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...
28%

MIAME Notation in Markup Language


MINiML (MIAME Notation in Markup Language, pronounced 'minimal') is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relation ...
28%

Immune Tolerance Network TrialShare


The immune tolerance data management and visualization portal for studies sponsored by the Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies a ...
28%

Minimum Information About a Peptide Array Experiment


These are preliminary guidelines describing the Minimum Information About a Peptide-Array Experiment (MIAPepAE). Described is a checklist of data and meta-data that should accompany a peptide-array experiment. The guidelines are maintained by the res ...
28%

Tissue Microarray Ontology


Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential ...
28%

PolyASite


Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...
28%

CycleBase


Gene expression profiles from cell-cycle microarray studies
28%

TcoF-DB


Database for Human Transcription Co-Factors
28%

RegPhos


Regulatory Network in Protein Phosphorylation
28%

A database for spatially resolved transcriptomes


Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved tran ...
28%

Real-time PCR Data Markup Language


The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML fil ...
28%

Recode


Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon red ...
28%

LungGENS


Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query retur ...
27%

NCBI Epigenomics


>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nucl ...
27%

Human siRNA database


HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup ...
27%

HLungDB


Database of Human Lung Cancer Research
27%

The Diatom EST Database


Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe. On this web site we present searchable databases of diatom ESTs (expressed ...
27%

YPA


YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...
27%

ncRNAs database


The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous ...
27%

Gene Expression Ontology


An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.
27%

Regulation of Gene Expression Ontolology


An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.
27%

KaPPA-View


Kazusa Plant Pathway Viewer
27%

PhytoMine


An InterMine interface to data from Phytozome
27%

Hardwood Genomics Project


The Hardwood Genomics Project is a databases for expressed genes, genetic markers, genetic linkage maps, and reference populations. It provides lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for ...
27%

Oryza Tag Line


Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.
27%

PmiRKB


Plant microRNA knowledge base
27%

Erythropoiesis Database


EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.
27%

ODB - Operon database


ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...
27%

TISSUES


TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda T ...
27%

WholeCellSimDB


WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: - Metabolite concentrations, - DNA, RNA and protein expression, - DNA-bound ...
27%

FlyBase Controlled Vocabulary


A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It provides a controlled vocabularies for use in annotation and classification of data related to Drosophila, including phenotypes and expr ...
27%

Minimum Information About a Spinal Cord Injury experiment


Standards for “Minimum Information about a Animal Spinal Cord Injury Experiment” (MIASCI) facilitates bioinformatic efforts and allow investigators to more accurately replicate and extend studies.
27%

PLANdbAffy


Probe-Level Annotation Database for Affymetrix microarrays
27%

Heart Diseases related Noncoding RNA Database


The Heart Disease-related Non-coding RNAs Database (HDncRNA) provides information about common heart diseases and their related noncoding RNAs. The HDncRNA database contains manually annotated associations of ncRNAs with heart disease. Sources of dat ...
27%

dbMAE


Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...
26%

SalmoBase


SalmoBase is an integrated molecular resource for Salmonid species which includes visualizations and analytic tools. The genome of the Atlantic salmon (Salmo salar) has undergone extensive restructuring since a whole genome duplication event ~80 mill ...
26%

Alternative Splicing Gallery


The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one ...
26%

FunSimMat


Gene Ontology-based functional similarity values for proteins and protein families
26%

DNA Methylation Database


The database contains information about the occurrence of methylated cytosines in the DNA.
26%

ViBrism DB


ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-base ...
26%

OryGenesDB: an interactive tool for rice reverse genetics


The aim of this Oryza sativa database was first to display sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. This ...
26%

EcoliWiki: A Wiki-based community resource for Escherichia coli


Community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
26%

DDPC


Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...
26%

miRGator v2.0


miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information about : 1) Human miRNA expr ...
26%

Stem Cell Commons


The Stem Cell Commons were initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with to ...
26%

H-DBAS


H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags have been generated from R ...
25%

Structural and functional annotation of Arabidopsis thaliana gene and protein families


GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
25%

Medaka Expression Pattern Database


MEPD contains expression data of genes and regulatory elements assayed in the Japanese killifish Medaka (Oryzias latipes).
25%

KnockTF


Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining targ ...
25%

MedicMine


MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.
24%

PeanutMine


PeanutMine integrates peanut data from LIS PeanutBase and other sources.
24%

BeanMine


This mine integrates many types of data for string bean built from the LIS chado database.
24%

LegumeMine


This mine integrates data for multiple legume species. It is under development by NCGR and is built from the LIS and PeanutBase chado databases as well as exports from other sources.
24%

WormMine


WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.
24%

LiceBase


LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.
24%

RatMine


RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.
24%

Life Science Database Archive


If a database is inadequate in terms of its description, unclear with respect to the terms of use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This is even true for databases with hig ...
24%

Aureolib


Proteomic signature library of Staphylococcus aureus Pathophysiology for inter-experimental expression data analyses.
24%

rSNP_Guide


A system of databases documenting the influence of mutations in regulatory gene regions.
24%

tRFexplorer


Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cel ...
24%

RaMP


A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.
24%

[email protected]


[email protected] is a microbial gene expression and comparative genomic database containing microarray datasets.
24%

Laminin Database


Laminins (LM) correspond to a large number of heretotrimeric glycoproteins, playing and a major role in several cell functions, including differentiation, proliferation, adhesion, and migration [1-3]. In addition to binding to other extracellular mat ...
24%

CoNekT-Plants


Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks
24%

Cnidarian Evolutionary Genomics Database


CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.
24%

ACID


The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...
24%

Full-parasites


Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources ...
24%

NIA Mouse cDNA Project


A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells was assembled. The cDNA libraries are freely distributed to the research community, providing a standard platform for expression studies using microarrays.
24%

AppleMDO


A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...
23%

PlantAPAdb


PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...
23%

SigReannot-mart


Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. The tool is a query environment populated with regularly updated annotations for different oligo sets. It permits easy extraction ...
23%

VDJbase


an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers eas ...
23%

PEATmoss


A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...
23%

GlyMDB


Glycan Microarray Database and Analysis Toolset.
23%

PlanExp


PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.
23%

circR2Disease


Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. March 31, 2018, the CircR2Disease has been updated. Circular RNAs (circRNAs) are widely expressed in diverse eukaryotic spec ...
23%

GTEx Portal


The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individua ...
23%

Signaling Pathways Project


The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...
23%

NimbleGen Gene Description


The NimbleGen Gene Description is a text tabular format that contains descriptive information (annotation) about the genes on an array. Please note that Roche issued a statement in 2012 as follows: "As previously announced in June 2012, Roche has exi ...
23%

CHD7 Database


The CHD7 mutation database contains, and is regularly updated with, anonymised data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype.
23%

Nimblegen Design File Format


NimbleGen Design File Format is a standard data file format. NimbleGen is now a trademark of Roche.
23%

Cell Signaling Technology Pathway Database


A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.
23%

microarray track data Browser Extensible Data Format


The microarray track data Browser Extensible Data Format displays configuration files for microarray annotation tracks displayed on the UCSC Genome Browser.
23%

Binary Probe Map Format


The BPMAP file contains information relating to the design of the Affymetrix tiling arrays. The format of the BPMAP file is a binary file with data stored in big-endian format.
23%

GenePix Results Format


The GenePix Results Format (GPR) contains general information about microarray image acquisition and analysis, as well as the data extracted from each individual feature. It was originally developed as the output format for GenePix software.
23%

AtFusionDB


Database of fusion transcripts in Arabidopsis thaliana.
23%

SCDevDB


A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database
22%

LanceletDB


Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.
22%

TCGA-LGG


Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.
22%

SCLD


User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.
22%

Daphnia stressor database


Taking advantage of a decade of Daphnia '-omics' data for gene annotation | Welcome to the Daphnia Stressor database
22%

GENSAT


The GENSAT (Gene Expression Nervous System ATlas) database captures information on gene expression in mouse brain at several developmental ages. The project began at Rockefeller University in New York under the direction of Nat Heintz, and has since ...
22%

GEISHA


GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe ...
22%

BioGPS


Gene annotation portal and a resource on gene and protein function
22%

MitoGenesisDB


Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis
22%

GRNdb


TF-target relationsips inferred from single cell and bulk RNA-seq datasets
22%

PEDE - Pig Expression Data Explorer


Full-length pig cDNA libraries and ESTs
22%

FlyTrap


Drosophila transgenic lines created using an intron protein trap strategy
22%

EBI resources


Database resources of the European Bioinformatics Institute
22%

Berkeley Drosophila Genome Project EST database


The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence.
22%

GabiPD


The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary in ...
22%

TBDB


Stanford Tuberculosis Database
22%

Monarch Initiative


Human disease-related phenotypes in model organisms
22%

Citrusgreening.org


Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating ...
22%

AOE


AOE (All Of gene Expression) - an integrated index for public gene expression databases.
21%

Genevestigator


High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drug ...
21%

CCLE GDSC


Databases which contain gene expression levels from next generation sequencing and also drug screening data for a large number of cancer cell lines.
21%

Nematode Expression Pattern DataBase


The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from ...
21%

MozAtlas


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.
21%

Hepamine


A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Providing Bioinformatics Data For The Study Of Liver Diseases. a liver disease microarray database, visualization platform and data-mining resource. Hepamine was ...
21%

GUDMAP


The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are: (1) a molecular atlas of gene expressi ...
21%

ErythronDB


The Erythron Database is a resource dedicated to facilitating better understanding of the cellular and molecular underpinnings of mammalian erythropoiesis. The resource is built upon a searchable database of gene expression in murine primitive and de ...
21%

HAHmiR DB


A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits. HAHmiR DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally vali ...
21%

EpiDB


Provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock. Future work will providedata tracks for these information sources and will ID tissue specific regulation information that is helpful in dissectin ...
21%

BaRTv1.0


Barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.
21%

EGMRG


Encyclopedia of microbiota regulated genes.
21%

Oral Cancer Gene Database


Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the s ...
21%

PCxN


Powerful new framework for interrogation of global pathway relationships.
21%

NCBI Nucleotide


The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.
21%

NetSlim


NetSlim is a resource of high-confidence signaling pathway maps derived from NetPath pathway reactions. 40-60% of the molecules and their reactions in NetPath pathways are available in NetSlim.
21%

RecountDB


A secondary database derived from primary data in NCBI's short read archive. Database for corrected read counts and genome mapping on NCBI's transcriptomics archives.
21%

Mammalian Transcriptomic Database


MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provid ...
21%

Gene4PD


a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.
21%

Cocoa Genome Hub


The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.
21%

FunGenES


A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.
21%

caArray


>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessib ...
21%

NCBI Third Party Annotation


TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the se ...
21%

Estonian Biocentre Free Data


A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.
21%

Avian Immunome DB


Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.
21%

Bibliome Variant Database


The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...
21%

LifeMap Discovery


LifeMap Discovery® is a compendium of embryonic development for stem cell research and regenerative medicine, constructed by integrating extensive molecular, cellular, anatomical and medical data curated from scientific literature and high-throughput ...
21%

ATAV


ATAV is a comprehensive platform for population-scale genomic analyses. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and single ...
21%

Birdbase


The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, i ...
21%

BART Cancer


BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...
21%

Brain Transcriptome Database


The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, functi ...
21%

Organelle Genome Megasequencing Program


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 gen ...
21%

Mouse Tumor Biology Database


The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, ...
21%

DSPR


The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different s ...
21%

NetPath


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 ...
21%

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