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Links tagged with 'gene expression'

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ArrayExpress updateDatabase Content

http://www.ebi.ac.uk/arrayexpress

Expression > Databases

The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

NAR Database Issue 2011
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tagsgene expression gene expression profiling genetic databases genomics high-throughput nucleotide sequencing oligonucleotide array sequence analysis

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

BgeeDatabase Content

http://bgee.unil.ch/

Expression > Databases
Model Organisms > Databases

Bgee is a dataBase for Gene Expression Evolution. It allows one to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.

This content is being maintained by bgee.

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tagsanatomical ontology anatomy bgee development developmental ontology evo-devo database evolution gene expression gene expression evolution' ontology

CancerResourceDatabase Content

http://bioinformatics.charite.de/cancerresource/

Other Molecules > Databases

CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine.

This content is being maintained by robertpreissner.

NAR Database Issue 2011
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tagsantineoplastic agents data mining gene expression humans neoplasm proteins protein databases systems integration tumor cell line

CIBEXDatabase Content

http://cibex.nig.ac.jp/

Expression > Transcript Expression Analysis

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

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tagscomputational biology database management systems forecasting gene expression gene expression profiling genetic databases information systems oligonucleotide array sequence analysis software design

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de

Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

NAR Database Issue 2011
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tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

COXPRESdbDatabase Content

http://coxpresdb.jp

Expression > Databases
Model Organisms > Databases

COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.

NAR Database Issue 2011
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tagsanimal models animals gene expression gene expression profiling gene regulatory networks genetic databases humans mice protein interaction mapping rats

DroIDDatabase Content

http://droidb.org/

DNA > Databases
Model Organisms > Databases
Protein > Databases

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

NAR Database Issue 2011
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tagsanimals drosophila drosophila proteins gene expression gene regulatory networks genetic databases insect genes micrornas protein interaction mapping systems integration transcription factors

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

EMAGEDatabase Content

http://www.emouseatlas.org/emage/

Expression > Databases
Model Organisms > Databases

EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

NAR Database Issue 2010
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tagsanimals automation computational biology database management systems developmental gene expression regulation embryonic development factual databases gene expression gene expression profiling genetic databases mammalian embryo mice molecular imaging nucleic acid databases programming languages

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

Ensembl GenomesDatabase Content

http://www.ensemblgenomes.org

Model Organisms > Databases

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

NAR Database Issue 2010
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tagsanimals anopheles gambiae bacterial genome classification computational biology fungal genome gene expression genetic databases genetic polymorphism genome humans invertebrates nucleic acid databases open reading frames plant genome search engine single nucleotide polymorphism tertiary protein structure

FlyBaseDatabase Content

http://flybase.bio.indiana.edu/

Model Organisms > Fly

FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.

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tagsanimals bibliography as topic california chromosome mapping computational biology drosophila drosophila melanogaster drosophila proteins europe factual databases gene expression gene library genetic databases genetic models genetic transcription genome insect genes mutation phenotype publishing research

Gene Expression Database (GXD)Database Content

http://www.informatics.jax.org

Expression > Databases
Model Organisms > Databases

The Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants. GXD places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases. Web-based query forms support simple or complex searches. All data are annotated and reviewed by GXD curators.

NAR Database Issue 2011
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tagsanimals gene expression genetic databases mice

GeneExpress2.1Tool Content

http://wwwmgs.bionet.nsc.ru/mgs/gnw/

Expression > Protein Expression
Protein > Interactions, Pathways, Enzymes
Protein > Protein Expression

Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD).

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tagsdatabase management systems gene expression programming languages systems integration