In this quick-and-dirty
demonstration of The Genomic HyperBrowser, you will count the number of genes in cytobands.
- Start by clicking "The Genomic HyperBrowser" and "Perform analysis" from the Tools menu
- Select the human genome (Human Mar. 2006 (hg18/NCBI36)
- Select "Genes and gene subsets", "Genes" and "CCDS" in the selection box for the first track.
CCDS is the gene definition that you will use in this demo.
- Select "-- No track (single track analysis) --" in the selection for for the second track.
This is because you will only analyze a single track in this example.
- Select "Counts" in the box for descriptive statistics.
A textual representation of the selected analysis appears, here: "The number of CCDS (Genes)"
- Select 'Compare in: "Cytobands"' in the "Region and scale" box.
- Keep the default "*", which means all cytobands.
- Click "Start analysis"
A "Perform analysis"
element appears in the history.
- Click the "eye" icon on the history element.
Some progress information
appears if the analysis is still running, which changes to the result table when the analysis is finished. Looking at the results, you can see that there is 16620 genes in the whole genome, according to the CCDS definition. In this case any genes that are overlapping, that is with different splice variants, are counted as one gene.
- Click "Html" under "Local analysis" and "Table: values per bin"
A table with the count of genes in all cytobands appears.
- Go back one page in your web browser (usually, a left-facing arrow in the top right corner).
- Click "Figure" under "Local analysis" and "Plot: values per bin"
A PDF-file appears, either inside your web browser, or as a downloaded file, depending on the particular setup of your computer. Each chromosome is plotted from its start to its end position. Each "box" corresponds to a cytoband, with its corresponding position and length. The height corresponds number of genes in that cytoband.