Max Planck Institute
for Heart and Lung Research

SNP4Disease Help

SNP4Disease is a knowledge database that was constructed using data and literature mining techniques to incorporate data from various publicly-available databases. It provides the information about disease associated SNPs and their potential biological impacts.





Search Terms

SNP4Disease provides 5 different ways to query the database.



Search by MeSH Term

To retrieve SNPs that are associated with a certain disease, you can either:
(1) Select a disease from the dynamically generated drop down menu, which is based on the tree structure of the MeSH database.
(2) Enter a disease in the lower text box.
In the first case, the definition of each MeSH term will be displayed in the text box located in the same window.

search for diseases


Compare MeSH Terms

To compare diseases for common SNPs, select the tab Compare MeSH Terms and enter the names of diseases to be compared.
If you would like to compare more than two diseases, press the [+] button, and another text box will appear.
After all the disease names are entered, press the [next] button to generate a Venn diagram.
To retrieve a list of SNPs, simply click on the intersection of your interest in the Venn diagram.

compare MeSH Terms


Search by SNPs

A search for the information about multiple SNPs can be executed by entering the rs_number of the
dbSNP database in the text box. Each rs_number should be separated by a comma.

search for SNPs


Search by Gene

If you are interested in certain genes, a search can be performed from the gene symbols or the
Entrez Gene IDs to retrieve the information about the SNPs that affect the selected genes.

search for Genes


Search by UniGene

To search for UniGene transcripts, enter the UniGene ID separated by comma.

search for Unigenes


Output options

The information from the following publicly-available databases can be added to annotate the searched SNPs:

-dbSNP (www.ncbi.nlm.nih.gov/snp)
-PubMed (www.ncbi.nlm.nih.gov/pubmed/)
-Entrez Gene (www.ncbi.nlm.nih.gov/gene)
-UniGene (www.ncbi.nlm.nih.gov/unigene)
and
-C-It (http://C-It.mpi-bn.mpg.de).


Filters

There are the following two filters available:

(1) Show only entries with the OMIM information
(2) Filter results by tissue
When the second filter is selected, additional information to be selected appear as shown below.

Filter

From the pull down menu, selected the tissue of your interest. The categories for tissues are based on those of the UniGene database (http://www.ncbi.nlm.nih.gov/UniGene/lbrowse2.cgi). The further filters can be set based on the expression profiles of the UniGene database.

After all the filters are specified, press the [search] button.


Result view

After the query to SNP4Disease has completed, the results will be displayed in a split window.
The upper part displays all disease associated SNPs with the previously selected information in the table format.
The lower part shows further information from the linked biomedical and genomic data sources for a selected SNP.
The size rations of the two parts can be freely changed by the user. In this way, it is possible to drill down to the fully extended primary information for a specific SNP without leaving the context of the original query.
The resulting table can be sorted according to various criteria (e.g. the number of publications) by clicking on the respective column header. This allows the user to find those SNPs that have been studied previously by others.
The result table can also be downloaded as a PDF-document or as comma separated values to save or process the dataset further.