Table 2.
Publicly accessible databases that disseminate information from microbial HTP experiments
| Single “-omic” | ||
|---|---|---|
| Dataset type | Database | Website |
| Gene expression | ||
| GEO | http://www.ncbi.nlm.nih.gov/geo/ | |
| Arrayexpress | http://www.ebi.ac.uk/arrayexpress | |
| Stanford Microarray | http://genome-www5.stanford.edu | |
| Database (SMD) Comprehensive Systems-Biology Database (CSB.DB) | http://csbdb.mpimp-golm.mpg.de/ | |
| Enzyme activity | ||
| Structural Proteomics in Torontoa | http://www.utoronto.ca/AlEdwardsLab/eg_list_of_enzymes.html | |
| PPI | ||
| Biological General Repository for Interaction Datasets (BioGRID)b | http://thebiogrid.org/ | |
| IntAct | http://www.ebi.ac.uk/intact/main.xhtml | |
| Agile Protein Interaction DataAnalyzer (APID)c | http://bioinfow.dep.usal.es/apid/index.htm | |
| Molecular INTeraction(MINT) | http://mint.bio.uniroma2.it/mint/Welcome.do | |
| DNA-binding | ||
| Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) | http://the_brain.bwh.harvard.edu/uniprobe/ | |
| Gene essentiality | ||
| Database of Essential Genes (DEG) | http://www.essentialgene.org/ | |
| Organism-centric that integrate HTP data | ||
| Organism | Database | Website |
| S. cerevisiae | SGD | http://www.yeastgenome.org/ |
| E. coli | eNet | http://ecoli.med.utoronto.ca/ |
| EchoBase | http://www.york.ac.uk/res/thomas/ | |
| EcoliHubd | http://ecolihub.org/ | |
| Ecoliwiki | http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki | |
| E. coli Interaction Database (EcID) | http://ecid.bioinfo.cnio.es/ | |
| Ecogene | http://www.ecogene.org/ | |
| Bacillus subtilis | B. subtilis Open Reading Frames (BSORF) | http://bacillus.genome.jp/ |
| Cyanobacteria | CyanoBase | http://genome.kazusa.or.jp/cyanobase |
| Plasmodium falciparum | PlasmoDraft | http://www.lirmm.fr/~dufayard/plasmo_draft_beta/ |
| Neisseria meningitidis | NeMeSys | http://www.genoscope.cns.fr/agc/microscope/expdata/nemesys.php |
| Multi-organism or integration of datasets | ||
| Database | Website | |
| Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) | http://dag.embl-heidelberg.de/newstring_cgi/show_input_page.pl | |
| PAThosystems Resource Integration Center (PATRIC) | http://wwww.patricbrc.org/portal/portal/patric/Home | |
| iProClass | http://pir.georgetown.edu/iproclass/ | |
| The SEED | http://theseed.uchicago.edu/FIG/ | |
a
Not a database, but does list results of HTP-enzyme screens.
b
Also contains data from genetic interaction datasets
c
PPI datasets from BIND (Biomolecular INteraction Network Database), BioGRID, DIP (Depository of Interacting Protiens), HPRD (Human Protein Resource Database), IntAct and MINT are included.
d
Searches 13 different web resources.