ChagasDB

I. Introduction

ChagasDB gathers all the molecules significantly associated with T.cruzi infection. All this information have been gathered by hand, by listing the papers referenced under "Chagas disease" in Pubmed, since 1945. For now, only the host-infected dysregulations were considering, discarding the genetic modified host, stimulated cells, or vector analysis.

Actually, a total of 24526 features were associated with Chagas disease, including gene, protein, methylation, hormone, electrolytes or chemical molecules expressions, as well as polymorphisms, haplogroups, protein activity or alternative splicing. 5 different organisms were studied: Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris and Ovis aries (see table below).

	Homo sapiens	Mus musculus	Rattus norvegicus	Canis lupus familiaris	Ovis aries
RNA	11954	5885	289	11	3
Alternative splicing	1778
Methylation	11169
TFBS	30
Polymorphism	49
Haplogroup	6
Protein	339	56	15	3
Protein activity	7	7
Chemical molecule	49	2	5
Electrolyte	1	2
Hormone	8

II. Database description

Feature name	Feature official name according to databases (see “Features annotation“ section).	Feature description	Description about the features which provide some details according to databases (see “Features annotation“ section). In some case, no description is available.
Feature name in papier	Feature name provided by authors. May be different to the official name.	Feature ID	Feature ID according to databases (see “Features annotation“ section). It may be Ensembl ID for genes or proteins, cg ID for methylation site or rs ID for polymorphisms. In some case, no ID is available.
Feature type	Type of the feature in the relative paper.	Feature variation	Some additional information about the analysis performed on the relative feature. It may be a fold change, or others kind of dysregulation.
Phenotype 1	Host phenotype associated with the relative feature dysregulation (see “Phenotypes available“ section).	Description phenotype 1	Additional information on the phenotype of interest.
Phenotype 2	Host phenotype used as control in the relative study. It may be identical to Phenotype 1 when the analysis was focus on association between two features.	Description phenotype 2	Additional information on the control phenotype (see “Phenotypes available“ section).
Tissue	Tissue or cells in which the feature of interest was studied.	Tissue description	Additional information on the tissue when provided.
Experimental	Indicate if the analysis is experimental or computational.	Method	Name or type of method employed to analyze the feature of interest.
Interaction observed	Indicate if an interaction/association was observed between the feature of interest and another feature.	Name of the interactive feature	If an interaction is observed between the feature of interest and another feature, indicate its name.
ID of the interactive feature	If an interaction is observed between the feature of interest and another feature, indicate its ID.	Type of the interactive feature	If an interaction is observed between the feature of interest and another feature, indicate its type.
Organism	Name of the species in which the analysis was carried out.	Population	Additional information on the population of interest.
T.cruzi strain	If known, provide the strain of T.cruzi having infected the host (see “T.cruzi strains“ section).	Paper PMID	Provide the paper Pubmed ID.
Paper DOI	Provide the paper DOI.	Paper title	Provide the paper title.
Paper publication date	Provide the paper publication date.

1. Features annotation

The features were annotated using different databases, depending on the species. For all of them, Ensembl database was used. For Homo sapiens specifically, HGNC and GeneCards helped to identify some alias. miRBase and LNCpedia were used for ncRNAs. The MGI and RGD were employed for Mus musculus and Rattus norvegicus, respectively.

2. Phenotypes available

For now, 19 phenotypes are available in ChagasDB: 5 as negative control (T.cruzi uninfected patients) and 14 as cases, with different forms of Chagas disease.
All phenotypes are listed below :

Phenotype description

Non-infected phenotypes

Healthy

Cardiomyopathy

Non chagasic cardiomyopathy Non chagasic dilated cardiomyopathy Idiopathic dilated cardiomyopathy Ischemic cardiomyopathy

T.cruzi infected phenotype

Chagas Acute stage Acute

Chronic stage

Chronic

Asymptomatic

Asymptomatic Indeterminate

Symptomatic

Cardiac

Cardiac Moderate cardiac Mild cardiac Severe cardiac Digestive Cardiodigestive Mixed Congenital infection Heart transplant chagasic patient

3. T.cruzi strains

24 Trypanosoma cruzi strains were included in the database, corresponding to 3 Discrete Typing Units (DTUs) :

TcI : Brazil, Colombia, G, Sylvio, SylvioX10/4, AC, CA-I, Col1.8G2, K98 and Type1.
TcII : ABC, Berenice-78, Y, JG, Lucky and SGO-Z12.
TC VI : CL-14, CL-Brener, Cvd, Q501/3, Tehuantepec, Tulahuén, RA and VD.

III. Database userguide

On the Database page, you have the possibility to manually search some information. You can enter a feature name, ID or description in the “Search” bar tool, and the different corresponding features will appears. By checking the boxes next to the feature name, you can download the information for your features of interest.

You have also the opportunities to apply some filters by clicking on the “Filter” buttons. It will allow you to restrains your research to some phenotypes, T.cruzi strains, tissue, or others fields of interest.

To provide a clear display of the results, some columns are automatically masked. You can display the columns of interest by clicking on the “Display” button, and check the boxes desired.

IV. Database submission

ChagasDB team updates the database periodically, to provide all interesting results to the community. However, you have also the opportunity to contribute to this research work. To do so, simply click on the "Submit" page and download the submission template. Once completed, you can submit it directly on the same page, by specifying your name and your email address. Our team will update the database with your data. You can also contact us if some information of one of your study are missing, or incomplete, and we will correct it in the database.