User Guide

The main web interface provides two ways to explore integrated disease-related information: the disease terms tree view and through query-searching.
The disease terms tree view consists of 23 top disease terms having an average of five or six sub-term classes.

  • Users can look over all the disease terms together in the tree view.
  • When users click a disease term, they can get results consisting of targeted disease-related information (disease name, synonyms, and title), and gene and SNP information associated with diseases directly.
  • To get more detail information about gene or SNP, users can explore with the gene symbol or SNP identifier (rs number) in genes or SNPs list results.
The web interface allows querying with three kinds of terms: 1) an SNP identifier (rs number from dbSNP), 2) a gene ID (symbol and description), or 3) a disease term. For an instance, we describe about retrieving query results with the gene symbol.

An SNP identifier
  1. When the user submits a SNP identifier, the system shows the gene, SNP, and disease information through genome browser (Gbrowse) generally. In addition, it provides more detail SNP information and effects such as SNP position on genome, SNP allele, SNP effects by using PolyPhen and SIFT, transcripts information in which the SNPs located, allele frequencies and flanking sequences from SNP resources.
A gene ID
  1. When the user submits a gene symbol, the system will return a list of genes related to the query with gene aliases and gene type.
  2. When selecting a specific gene, query results show the gene, its transcripts, SNPs and genetic variants through the genome browser. The genome browser is available to provide insight into genetic variants’ effects on transcripts. Transcripts and SNP marker information displayed in the genome browser facilitates the recognition of the characteristics of disease-causing genes, especially if the SNP or genetic variation lies in the promoters or in an intronic sequence.
  3. A disease term
A disease term
  1. When the user submits a disease, the system will return disease terms list for the query disease and disease description. Also, it provides genes list and SNPs list associated with query disease.
  2. When selecting a specific gene or SNP identifier, query results show more detailed information about gene or SNP while displaying the results through the genome browser.




Figure1. Web Interface

The main page consists of two parts; a part with a search engine using keywords and a part for the three view of disease terms. In the key-word search engine, the web interface allows for queries based on three types of information: SNP identifier (rs number from dbSNP), gene (Gene name, gene symbol, refSeq ID), or disease term. By using the tree view of disease terms, a user can look over all the categories of diseases involving genes and genetic variations. Diseases that have been of great research interest such as diabetes mellitus, breast cancer, and Parkinson disease are represented at the top right of the web interface.



Figure2. Query table results and graphic viewer

The retrieval page of the integrated diseases database. The information on diseases, genes, and SNP markers found as results for a query are shown in (A). If a user wants more specific information about each result, the user can click each disease tern, gene ID, or genetic variation number (SNP rs number). When a user clicks the gene symbol in a gene result table, this retrieves the Gene Information table, which shows various gene annotations, including transcript gene structure and the location of the genetic variation in the human genome (B).

(A)

(B)