Endometriosis Knowledgebase


A repository for genes associated with endometriosis

Help


The Fe has user friendly search engine. The different options are described below in detail


Search

Simple search
The simple search option allows the user to type any keyword in the text box and on submission searches the entire database for enties similar to the user entered keyword

Advanced search


Section Search Fields Examples
Gene Gene symbol Eg: AMH
Gene Name Eg: anti-Mullerian hormone
Chromosome Eg: 19
Chromosome location Eg: 19p13.3
Gene description Eg: infertility (Any information related to role/function of the gene)
Protein Uniprot accession Eg: P01225
Gene Symbol Eg: USP9Y
Protein name Eg: Follicle-stimulating hormone beta subunit
Protein length Eg: 141
Sequence Eg: MAAYQQEEQM (You could search partial or complete sequence)
Variant Eg: rs751299877
Pathway Eg: Lipid metabolism; (Search by pathway name)
Tissue specificity Eg: brain (Search by tissue)
PDB accession 2F8A (Search by PDB accession)
MINT MINT-1393072 (Search by MINT database accession)
STRING ENSP00000344460 (Search by STRING accession)
Entrez Gene accession Eg: 8287 (Search by entrez gene id)
KEGG accession Eg: hsa:3294 (Search by KEGG accession)
GeneCards accession Eg: AMH (Search by gene symbol)
MalaCards Eg: AMH (Search by gene symbol)
SNP SNP accession Eg: rs16
SNP accession Eg: rs16
Gene Symbol Eg: AMH
Upstream sequence Search by sequence upstream to the SNP (single letter amino acid code)
SNP Eg: A/G (Search by allele change)
Downstream Search by sequence downstream to the SNP (single letter amino acid code)
Hgvs Search by NCBI's nucleotide, proein accession id
Hgvs Search by NCBI's nucleotide, proein accession id
Mutation type Eg: snp, in-del
Sub mutation type Eg: intron-variant, frameshift, missense etc.
Clinical significance Eg: Pathogenic or Benign
GO Entrez gene accession Eg: 8287
Go category Eg: molecular function, biological process or cellular component
Evidence code Eg: TAS, IPI, NAS
GO id Eg: GO:0005179
GO term name Eg: hormone activity
KEGG Pathways Entrez gene accession Eg: 8287
Entrez gene symbol Eg: AMH
KEGG Pathway id Eg: hsa04080
KEGG Pathway name Eg: Neuroactive ligand-receptor interation, Metaboli Pathways
Diseases Entrez gene accession Eg: 8287
Entrez gene symbol Eg: AMH
KEGG disease name Eg: PCOS
Literature references Entrez gene accession Eg: 8287
PubMed id Eg: 26389512
Infertility condition Eg: PCOS
Ethnicity Eg: Chinese, Indian etc.
Infertility type Eg: Female, Male


Browse

The browse option allows users to browse:

Genes: by gene symbol or gene name

Proteins: by gene symbol or protein name

SNPs: by gene symbol or NCBI SNP database accession id

Reference Literature: by gene symbol or PubMed id

Gene Ontology: by GO term name or gene symbols

Diseases: by gene symbol or Diseases

Pathways: by gene symbol or KEGG Pathways

Tools

CDART: This tool helps in identifying protein domains in the user selected genes

STRING: This tool helps in identifying interacting proteins among the user selected genes

MOTIF SCAN : This tool helps in identifying protein MOTIFS in the user selected genes

SNPs: This tool carries out SNP analysis (maps to chromosome positions, genes and predicts variant effects) the for the user selected SNPs using g:Profiler (SNPsense)

ORTHOLOGS: This tool helps in identifying orthologs for the user selected genes using g:Prolfiler (g:ORTH)

BLAST

BLASTN: This tool helps in carrying out a nucleotide blast for a set of user selected genes using NCBI BLASTN program

BLASTP: This tool helps in carrying out a protein blast for a set of user selected genes using NCBI BLASTP program

Analysis

DISEASES: This tool alows user to select a group of genes and find common diseases among them. The gene disease associations are taken from GAD, OMIM and Female Infertility Knowledbase

PATHWAYS: This tool alows user to select a group of genes and find common pathways among them. The gene pathways associations are taken from the KEGG database

GO: This tool alows user to select a group of genes and find common gene ontology among them. The gene ontology associations are taken from the AmiGO database

Function: This tool alows user to select a group of genes and carry out functional profiling like statistical enrichment analysis on GO terms, human disease gene annotations and protein-protein interaction networks

PANTHER: This tool alows user to select a group of genes and find enriched gene ontology and pathways using the PANTHER tool

Statistics

The statistics page gives the number of genes, proteins, snps, gene ontology, pathways and diseases in the database