Help
The Male infertility database has usesr 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 |
| Gene Symbol | Eg: AMH | |
| SNP | Eg: A/G (Search by allele change) | |
| Hgvs | Search by NCBI's nucleotide, protein accession id | |
| Mutation type | Eg: snp, in-del | |
| Sub mutation type | Eg: intron-variant, frameshift, missense etc. | |
| Associated diseases | 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 | |
| Disease name | Eg: Cryptorchidism | |
| Literature references | Entrez gene accession | Eg: 8287 |
| PubMed id | Eg: 26389512 | |
| Infertility condition | Eg: Cryptorchidism | |
| Ethnicity | Eg: Chinese, Indian etc. |
Search Syndromes
Users can use this option to find phenotypes associated with syndromes and their associated genetic defect(if reported)
Search Chromosomal defects
Users can use this option to find chromosomal defectassociated with male infertility.
Search Infertility phenotypes
Here the users can search the validated dataset of MIK for genes associated with the 21 broad disease groups.
Search Highthroughput Dataset
Users can search the gene-diseases association in the Highthroughput dataset of MIK and also retrieve the gene prioritization rank obtained using the disease specific validated dataset of MIK as the training dataset based on
Functional information (Gene ontology(BP, CC, MF), Pathways, Coexpression, Human Phenotype)
Protein-Protein interaction network (based on there proximity and iteractions with genes in the validated dataset of MIK)
*The above scores/ pvalues are obtained from ToppGeneSuite
Number of literation Reference: Here the genes are prioritized based on the number of references for a particular gene-disease association in the Highthroughput dataset of MIK
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