TrypsNetDB

Frequently Asked Questions


What type of interactions are present in the database?
How to filter the network to represent interactions supported by specific techniques?
Which trypanosomatid organisms are supported?
How the ortholog mapping is conducted?
What identifiers are supported?
What is the color coding of proteins in the network?
Why size of protein nodes vary?
Why some proteins have red background in proteins submenu?
How to select the first neighbours of a protein in the network?
What resources are used for the geneset enrichment analysis?
Are reported p-values corrected for multiple testing?
What are the numbers in the menu of genome-wide data?
How to save the results?
How to reproduce the results?
How to query the database programatically?


What type of interactions are present in the database?
The current release of the database is focused on physical protein interaction data that are already published in trypanosomatid field. The detailed list of supported interactions is present in the statistics section of the database. The list of publications that were used for the extraction of protein interaction data are also available in the Refernces section of the database.

How to filter the network to represent interactions supported by specific techniques?
In the network section, uncheck the interaction types that you are not interested in and then click on "Set filters".

Which trypanosomatid organisms are supported?
The current release supports 16 trypanosomatid parasites including T. cruzi strain CL Brener, T. cruzi CL Brener Esmeraldo-like, T. cruzi CL Brener Non-Esmeraldo-like, T. brucei gambiense DAL972, T. brucei Lister strain 427, T. vivax Y486, T. evansi strain STIB 805, T. brucei TREU927, L. major strain Friedlin, L. mexicana MHOM/GT/2001/U1103, L. infantum JPCM5, L. donovani BPK282A1, L. braziliensis MHOM/BR/75/M2903, L. braziliensis MHOM/BR/75/M2904, L. arabica strain LEM1108, L. enriettii strain LEM3045. Support for the rest of trypanosomatid species are scheduled to be added in the coming months. For more details, please see the statistics section of the database.

How the ortholog mapping is conducted?
We have only considered syntenic orthologs reported by TriTrypDB to transfer the inter-species information.

What identifiers are supported?
The database can be queried based on either tritrypDB IDs (recognizing IDs of recent and older versions of the database) or gene names. In cases that gene names match to multiple organisms, the user will be asked to select the species of interest from a dropdown box.

What is the color coding of proteins in the network?
Queried proteins have blue background and the suggested interacting partners by the database are in gray.

Why size of protein nodes vary?
The size of protein nodes is positively correlated with the number of interactions that the protein has in the global network. So highly interacting proteins have larger node size than those with smaller number of interacting partners.

Why some proteins have red background in proteins submenu?
Those queried proteins with no recorded interacting partner are highlighted with red color.

How to select the first neighbours of a protein in the network?
Clicking on a protein will highlight the first neighbors of that protein and open the corresponding information in the proteins tab of the information panel.

What resources are used for the geneset enrichment analysis?
Proteins present in the network are tested for the enrichment for the below categories:
Functional analysis: Gene ontology, KEGG pathway, and BioCyc annotations.
Biological responses: the proteins are tested for their collectinve response in terms of transcriptome, proteome, and essentiality across more than 50 different conditions.
Sequence & Structure: protein motifs, isoelectric points, molecular weights, and predicted number of transmembrane domains
3′ regulatory elements: computationally predicted functional regulatory elements

Are reported p-values corrected for multiple testing?
In cases that correction for multiple testing is required, the database reports Benjamini-Hochberg corrected p-values and states "Corrected p-value".

What are the numbers in the menu of genome-wide data?
The numbers in the menu of genome-wide data indicate the number of proteins that have such data.

How to save the results?
By going to the save option on top of the network section, you are able to save the whole represented network or only the sub-networks that are supported by a specific experimental technique. It is also possible to save the enrichment analysis results as well as annotations of genes such as description, transcript or protein characteristics (length, weight, isoelectric point, identified SNPs), and gene ontology.

How to reproduce the results?
by going to the save option on top of the network section, you can save the query list. Using the same query, the database will reproduce the same results.

How to query the database programatically?
The database can be queried directly by using the following URL:
http://trypsnetdb.org/extQuery.aspx?Id=<Comma_Separated_Gene_Identifiers>
example:
http://trypsnetdb.org/extQuery.aspx?Id=Tb927.10.8210,Tb927.9.4360,Tb927.2.2470