Help

1. Quick Search

Quick search option in PCOSKB allows users to search whole database based on keywords, the hits in each section of database are listed as result so the user by clicking on hit number can directly go to the respective section and see the list of hits. Searches using Boolean operators are possible using the Advance search option.

2. Advance search

Advance Search in PCOSDB allows users to search the database sectionwise by selecting fields and applying logical operators (AND, OR, NOT).

Section Fields Detail
Gene Information Gene Symbol HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols
Gene Name HUGO Gene Nomenclature Committee (HGNC) assigned unique gene name
Entrez Gene ID  
Chromosomal Location Location of gene in genome
Gene Summary Entrez Gene Summary
GeneCards ID  
UniGene UniGene ID
RefSeq DNA RefSeq DNA ID
RefSeq mRNA RefSeq mRNA ID
Protein Information Protein Name The name recommended by UniProt consortium
Function Described function of protein in UniProt
Refseq Proteins Refseq Proteins ID
UniProt UniProt ID
RCSB PDB RCSB PDB ID
Interpro ID  
Gene Ontology (GO) Gene Gene Symbol of gene
GO ID  
Ontology  
Definition  
Associated Diseases Gene Gene Symbol of gene
Disease  
SNP Gene Gene Symbol of gene
SNP ID  
Upstream Sequence Upstream Sequence of SNP
SNP  
Downstream Sequence Downstream Sequence of SNP
References Pubmed ID  
Title Title of publication
Author Author of publication
Abstract Abstract of publication
Source Original source of publication

Example:-

Browse
 

The browse option of the database is explained below:

Gene: All the genes present in the database can be browsed. Links to complete information on these genes is also provided. Alternatively there is also a search tab which will aid users in searching for a specific gene. An option to browse by alphabet has also been provided.

SNPs: This option lists all SNPs associated with PCOS, along with links to reference literature and dbSNP database. The search tab provided on this page allows search by gene or SNP ID.

Associated Diseases: The diseases associated with genes present in the database can be viewed using this option. The search tab will aid users in searching for specific diseases.

Pathways: The different metabolic/signalling pathways associated with genes in the database can be browsed. Links to KEGG pathway database is provided here. The search tab allows search of specific pathways.

Ontology terms: The different ontology terms associated with genes in the database can be browsed here. This page displays information on the different ontology terms present in the database, the genes annotated with those ontology terms and the pathways and diseases that the gene is associated with.

Tools

The tools section of the database is divided into two sections a) Gene based b) Disease based as described below:

Gene based: The gene based option allows users to analyse the gene-list for common pathways, diseases and ontology terms.

Disease based: This option allows users to retrieve information on genes in the database, their corresponding ontology terms and pathways associated with the user selected disease category. The results of this section displays all diseases grouped under the selected disease category and the genes associated with them.

Analysis

The analysis section is divided into four sections as described below:

Associated diseases with PCOS: A pie-chart representing the percentage of genes associated with a specific disease category can be visualized here. The genes associated with diseases grouped under the disease category can be accessed by clicking on the respective disease category in the pie-chart.

Pathways: A bar graph of all the pathways that are present in the database is displayed under the pathways section. The number of genes playing a role in each of these pathways is displayed at the top of the bar. The bar representing each pathway is hyperlinked to the KEGG pathway database.

Genes associated with major phenotypes: This section gives the total number of genes associated with PCOS and the most commonly associated phenotypes with PCOS. The genes associated with pathophysiology of these phenotypes can be accessed by clicking on the key provided.

Ontology terms: The ontology terms associated with genes in PCOSKB is represented as a pie-chart. The pie-chart is hyperlinked to the subcategories within each category.

 

 

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