Visualization Tools For Gene-Wide Results

Question

[Joey]

Hi All,

Can you suggest any visualization tools for gene-wide results?

I have some gene-wide results which i would like to plot (rather than putting the results in a big table). The raw data was at SNP-level.

My results file contains the following fields: Chromosome, Gene, P-value (for that gene), Gene start position, Gene end position

Also, are there any free tools out there which can take gene-wide p-values and perform pathway analysis based on that?

Thanks,

-Joey

[sentausa]

Didn't you mean genome-wide result?

Answer 1

[Sandeep]

Depending if the data is for human or other species, you can use UCSC genome graphs (include multiple tracks from UCSC), ideographica (represent the locus on a ideogram), CIRCOS (a command line based software on linux) or various other genome wide graphical tools as mentioned in Drawing Chromosome Ideogams With Data

For pathway analysis you can use DAVID (http://david.abcc.ncifcrf.gov/), Gene Set Analysis Toolkit (http://bioinfo.vanderbilt.edu/webgestalt/) or other gene ontology web servers that have options for pathway analysis. Both the above mentioned web tools use the genes and represent them on KEGG pathways based on their p-value significance.