In this exercise, user can learn how to search and retrieve gene details from NCBI Gene database.
Search by Gene Name:
Search for Akt1 gene in Homo sapiens
1. Open the NCBI homepage by clicking into the link http://www.ncbi.nlm.nih.gov/ (Figure 1)
Figure 1: NCBI Homepage
2. Select Gene from the drop down menu options of "All Databases". . In the query box, user can either type the name of the gene or disease name or any word which will display the list of genes of the entire organism associate with that query word. Here in this example, the user searches for the gene AKTI as shown Figure 2.
Figure 2: Selecting Gene from the drop down menu options
3. The display page will contain the result. User can make their selection by clicking on the results displayed (Figure 3).
Figure 3: Displaying the results
4. The result will display the details associated with that particular gene of interest. User can select different display options by clicking on the “Full Report” on the top of the result page (Figure 4).
Figure 4: Full Report display of the gene
5. The ‘Full Report’ will give detailed information including official symbol and its name, primary source, gene type, RefSeq status, organism name, lineage, other names for the gene, and the summary.
6. The ‘Genomic context’ displays location of the gene on the chromosome. Here it is displayed on the Chromosome No: 14. The Epigenomics view displayed on the right side gives the information about the experiments conducted in the genes to identify different modifications like DNA methylation etc. (shown in Figure 5).
Figure 5: The Genomics context and Epigenomic view
7. The ‘Map Viewer’ enables to view and search organism’s complete genome, neighbour genes, chromosome maps. The Zooming options on the bottom left side of the page allow the user to view the map into different levels in detail as shown in Figure 6.
Figure 6: Map Viewer
8. The Genomic context, transcripts, and products provide the gene and its neighbour’s information in a diagrammatic view. The RefSeqs displays coding regions and RNA products, the gene’s intron/exon organization. User can also view the graphic report, FASTA sequence view and the Gen Bank view for the particular gene.
Figure 7: Diagrammatic view of Genomic context