fitSNPs

Category Genomics>Genetic Data Analysis/Tools

Abstract fitSNPs (functionally interpolating Single Nucleotide Polymorphisms) is a web-based system that can be used to prioritize 'disease genes' from genome-wide association studies (GWASs) for multiple disease types and to predict disease associations for genes with high differential expression ratio (DER) values.

The manufacturer analyzed all human microarray studies from the NCBI Gene Expression Omnibus (GEO) (see G6G Abstract Number 20013), and found that differentially expressed genes were more likely to have disease-associated variants.

The more experiments in which a gene was differentially expressed, the more likely it contained disease-associated variants.

Based on this property, the manufacturer derived a list of functionally interpolating SNPs (fitSNPs) to prioritize genes for disease association, and successfully prioritized type 1 diabetes genes from the top 7 loci of Wellcome Trust Case Control Consortium GWAS.

fitSNPs contains a list of human Entrez Gene IDs with DER values.

Genes with disease-associated variants and corresponding diseases were retrieved from Human Gene Mutation Database (HGMD) and Genetic Association Database (GAD) (see G6G Abstract Number 20314).

To facilitate integration between fitSNPs and GWASs on the human genome, all reference SNPs were downloaded from dbSNP (the NCBI database of genetic variation) and assigned DER scores according to their associated genes.

For SNPs mapping to multiple genes, the highest DER value was selected.

fitSNPs can be loaded into the UCSC genome graph, in accordance with the instructions in the GWAS page of the fitSNPs server. It will automatically show up as a custom track in the UCSC Genome Browser (see G6G Abstract Number 20197) that can be compared with a wealth of genomic data, including multiple GWAS study results (see below).

fitSNPs Gene page features/capabilities --

On the Gene page, all human genes are sorted by their likelihoods to have disease-associated variants along with experimentally confirmed disease association if any. The likelihood is estimated by their DERs.

The higher DER a gene has, the more likely it will contain disease- associated variants.

By clicking the DER values, you can retrieve all microarray studies where this gene was differentially expressed. By clicking GAD, you can retrieve the experimental evidence for its disease association.

1) The Server displays all the records when the user clicks on the Gene menu. The user can further filter records using the Search functionality.

2) Next to the "Search" button, the "Navigation panel" with four (4) buttons is present. The user can navigate through all the pages by clicking these four (4) buttons.

3) The user can sort all the records by Gene, DER, Disease and GAD by clicking on the column header.

4) The system displays the order of sorting via an arrow.

5) The user can search by Gene Symbol or keyword for disease name.

6) The default option for the search functionality is 'Search by Gene Symbol'.

7) Search by disease keyword allows the user to enter a keyword or part of a keyword/disease name. e.g. "neuro"

8) Search by description keyword allows the user to enter a keyword or part of a keyword/description. e.g. "receptor"

9) The user can click on an individual Gene Symbol to get gene information from NCBI's Gene database.

10) The user can click on the 'GAD id' to get information from the Genetic Association database.

11) The user can click on the DER value to submit a relative Gene ID to the Bindin-gene server with a default q value of 0.05.

fitSNPs GWAS page --

The GWAS page describes a simple step-by-step tutorial to load fitSNPs into a UCSC genome graph and visualize it along with your genomic data, such as GWAS data.

fitSNPs Prediction page features/capabilities --

Some highly differentially expressed genes have Not yet been associated with any disease, and are interesting investigative leads.

The manufacturer used fitSNPs to prioritize genes for diseases with previously identified loci and an unknown molecular basis from the Online Mendelian Inheritance in Man (OMIM) database, and suggested 2,586 genes to be sequenced for 597 syndromes in the Prediction page.

1) The Server displays all the records when the user clicks on the Prediction menu. The user can further filter records using the Search functionality.

2) Next to the "Search" button, the "Navigation panel" with four (4) buttons is present. The user can navigate through all the pages by clicking these four (4) buttons.

3) The user can sort all the records by Disorder, Loci, Score, Gene and DER by clicking on the column header.

4) The system displays the order of sorting via an arrow.

5) The user can search by Gene Symbol or keyword for disease name.

6) The default option for the search functionality is 'Search by Disorder keyword'.

7) Search by disorder/description keyword allows the user to enter a keyword or part of a keyword/disease name. e.g. "neuro"

8) Search by Loci allows the user to input a Locus or part of a Locus. e. g. "21q22"

9) The user can click on an individual Gene Symbol to get gene information from NCBI's Gene database.

10) The user can click on the Disorder to get information from NCBI's OMIM database.

11) The user can click on the DER value to submit a relative Gene ID to the Bindin-gene server with a default q value of 0.05.

fitSNPs downloads --

1) The user can download fitSNPs DER values for all human genes.

2) The manufacturer predicted 2,586 genes to be associated with 597 syndromes with identified loci and an unknown molecular basis from OMIM using fitSNPs.

And, the user can also download the full Prediction list.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site fitSNPs

Price Contact manufacturer.

G6G Abstract Number 20431

G6G Manufacturer Number 104059