Search for genes/targets

Use this form to search for proteins/targets using any of the following criteria. Note that all selected criteria will be evaluated as the intersection (boolean 'AND') of the respective result sets. You can read more about this SEARCH page in the User's Manual.

2. Filter targets based on:

Name
Identifier/Accession
EC number
Gene Ontology
Pfam / Interpro domains
GO Slim Category
KEGG high-level pathway  
KEGG detailed pathway    
Protein length (AA)  
Molecular weight  
Isoelectric point
# of transmembrane (TM) spans
Signal peptide
GPI Anchor  
Retrieve targets with three dimensional data from  
Crystal structures (PDB) Structural models (from Modbase)
Number of models (at least)
Mycobacterium tuberculosis
Entamoeba histolytica
Leishmania major
Plasmodium berghei
Trypanosoma cruzi
Toxoplasma gondii
Trypanosoma brucei
Plasmodium falciparum
Plasmodium vivax

Notes on available datasets:



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Expression evidence was collected from several microarray and/or RNA-seq experiments and combined in a simplified scheme. Genes were grouped in 5 categories depending on how much upregulation they showed in the selected life cycle stage or experimental condition: 0-20%, 20-40%, 40-60%, 60-80% and 80-100%. With 0-20% representing the lower 20% of genes, showing less upregulation in the corresponding life cycle stage; and 80-100% representing the top 20% of genes (i.e. those showing a higher upregulation).

More detailed queries (fine grained) on gene expression can be performed with the original datasets at their respective sources (PlasmoDB, TriTrypDB, etc.).

Restrict to targets with orthologs (present/absent) in:

A. thaliana B. bovis B. malayi
C. albicans C. elegans C. hominis
C. parvum C. trachomatis D. discoideum
D. melanogaster E. coli E. granulosus
E. histolytica E. multilocularis G. lamblia
H. sapiens L. braziliensis L. donovani
L. infantum L. major L. mexicana
L. Loa (eye worm) M. leprae M. musculus
M. tuberculosis M. ulcerans N. caninum
O. sativa O. volvulus P. berghei
P. falciparum P. knowlesi P. vivax
P. yoelii S. cerevisiae S. japonicum
S. mansoni S. mediterranea T. brucei gambiense
T. brucei T. congolense T. cruzi
T. gondii T. pallidum T. parva
T. vaginalis W. endosymbiont of Brugia malayi
Number of Paralogs

Retrieve targets for which genome-wide information about their essentiality is available.
If genome-wide information for an organism is not available, you can evaluate the essentiality of the corresponding orthologs by selecting a different species from the options below. Also note that essential genes for your organism of interest might show up during manual curation (check the Validation data search option further down).

Any evidence of essentiality in any species

Or

Select the species and the type of 'essential' phenotype from the options below: note that if you select more than one option, the resulting set of genes will be the UNION (boolean OR) of the selection.

C. elegans

E. coli

M. tuberculosis

P. berghei

S. cerevisiae

T. brucei

T. gondii

Note that the ongoing curation effort will be producing curated data for all WHO target organisms. At this moment curated information is currently limited to T. brucei, L. major, T. cruzi,P. falciparum, and S. mansoni. Curated data from other organisms will be made available soon.

Any form of validation
Genetic validation
Pharmacological validation
Observed Phenotype

Toggle advanced search form (recommended for expert users) What's this?

Phenotype Advanced Form

You can use the advanced form to further refine your phenotype filtering

Note that you cannot use both the simplified form above and the advanced form below at the same time. This will produce unpredictable results! You have been warned!

To annotate phenotypes and/or validation experiments, we are using a phenotype syntax composed of terms derived from a number of controlled vocabularies (i.e. ontologies, e.g. GO, PATO, ECO). The syntax we are using is similar in spirit to the Pheno-syntax format described by Chris Mungall, although we have not attempted to formally comply with the pheno-syntax grammar.

The syntax consists of a collection of tag-values. Tags are i) the phenotypic quality or attribute (Q), ii) the entity bearing the phenotype (B), iii) an anatomy term that describes where the phenotype occurs (A) — not relevant for unicellular organisms, and iv) a term describing the timing during which the phenotype occurs (T) – usually a developmental stage.

As an example, the way to describe "slow growth in bloodstream forms" using this syntax is:

  • Phenotypic Quality (Q) = slow
  • Affected entity (B) = growth
  • During (T) = bloodstream form
  • Where (A) = whole organism

In this case the affected entity is growth and the way in which the growth is affected is described by the Q term (slow in this case), and this phenotype occurs in the whole organism.

The form below gives you access to search for targets using any of the terms we have used to annotate them. Do note that only a few combinations of Q, B, A, and T terms are represented in the db, even though you can search for all of them!

Phenotype

Affected entity
Phenotypic quality
Where (anatomic term)
When (time term)

Validation

Validation

Phenotypes/Validation

Evidence
Observed in
Validation
Network Druggability Score
Associated compounds

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The druggability index query lets you restrict your search based on a druggability measure.

The Network Druggability Score (NDS) is a TDR Targets proxy for druggability, calculated using Berenstein et al (2017) approach for drug repurposing. The NDS score is a float number, ranging from 0 to 1, that represents the degree of connections between a given protein and other proteins which are known druggable targets: the higher the degree, the higher the NDS. We have stratified druggability into groups (or Tiers), that range from 1 to 5, being 1 the least likely to be druggable, and 5 the most. Tiers are assigned according to their corrsponding NDS, and the number of thresholds this NDS is above of:

  • Tier 1: Targets with an NDS between zero and the noise threshold, which is calculated as ten times the mean value of the lowest 25% of the values.
  • Tier 2: Targets with an NDS between the noise and the Youden Cutoff threshold (Y), which is calculated from the Youden's J index obtained during ROC validations (when possible; or derived from the closest species Youden's J index available).
  • Tier 3: Targets with an NDS between the Youden Cutoff threshold and 10 times this value.
  • Tier 4: Targets with an NDS between the 10 times the Youden Cutoff threshold and 100 times this value.
  • Tier 5: Targets with an NDS greater than 100 times the Youden Cutoff threshold.

It is important to address that whether an NDS is "high" or "low" is species dependant (e.g: Highest NDS in Trypanosoma cruzi is 0.24, for Tier 5 TcCLB.509153.90 target), which implies that NDS values are only comparable within a given species.

It is also important to note that a known druggable target is almost guaranteed to be a top tiered (>3) target, but a low tiered target is not necessarily a non-druggable target

Associated compounds: associations between genes and chemical compounds are derived from a number of sources. In each case the association between a gene and a compound has been done by different methods, and thus the reliability and/or the relevance of the association is different for each source. You may use this to filter targets based on:

  • Manual curation (more reliable, more relevant)
  • Similarity or orthology extrapolated compounds from gene A based on its similarity to a gene B for which there are known compounds.
  • Network Derived Putative Interactions which derive from the NDS calculations (described above) but are done exclussively for orphan compounds (those that are active against a given pathogen but whose molecular target is yet unknown).
Assay available
Reagent available

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Assay available is currently evaluated as positive if the target is an enzyme, and if the enzyme has an assay described in the list of enzyme assays available from Sigma-Aldrich or if the pathogen protein has been assayed according to the BRENDA database.

Reagent available is evaluated as positive if the pathogen protein has been cloned or purified according to the BRENDA database or if recombinant, soluble protein has been produced by the Consortium for Structural Genomics of Pathogenic Protozoa. This is based on their ability to express the protein in an heterologous system (usually E. coli) in soluble form. You can check the status of their progress here.

Only search for genes for which we have mapped publications in PubMed

In PubMed

Or

Search for genes associated with a particular publication

Title
PubMed ID
Journal
Volume
Year
Pages