Pathway Graphs for gene set from RNA-seq

Question

[a.james]

Hello All,

I would like to display the data from results in a graphical way rfom the functional pathway analysis.

I have tried several R packages like KEGGgraph , PAthview, But they have there own input data format.

My data looks like this, where first col is genes and second column is the pathway enriched .

ALDH7A1; BPGM;          hsa00010: Glycolysis / Gluconeogenesis
ALDH7A1;                hsa00053: Ascorbate and aldarate metabolism
ACSL6; ALDH7A1;         hsa00071: Fatty acid metabolism
SOAT2;                  hsa00100: Steroid biosynthesis
PDE7B; GMPR; PDE4B;     hsa00230: Purine metabolism
UPP1;                   hsa00240: Pyrimidine metabolism
ALAS2; ALDH7A1; BPGM;   hsa00260: Glycine
TST;                    hsa00270: Cysteine and methionine metabolism
ALDH7A1; BCAT1;         hsa00280: Valine
BCAT1;                  hsa00290: Valine
ALDH7A1;                hsa00300: Lysine biosynthesis
ALDH7A1;                hsa00310: Lysine degradation

So in there are many pathways were more than one gene is involved .. For this kind of data is there any available method for data display I want it in pathway graphs not as bar plots.

Thank you so much for help

[karl.stamm]

>> But they have their own input data format.

A big part of the job is restructuring or re-organizing data. That's unrelated to graph displays.

[a.james]

Thank you ppl. I will look into all the solutions

[liupfskygre]

By the way, what tools did you use to do pathway enrichment analysis? Have you done GO enrichment?

Thanks!

[bigmawen]

You may try GAGE for both pathway and GO analysis if you know R. It supports ~3000 KEGG species, and 19 GO species.:

http://www.bioconductor.org/packages/release/bioc/html/gage.html

It works with well with Pathview.

[liupfskygre]

OK, thanks!

[EagleEye]

If you want to find GO or Pathway enrichment for your set of genes you can try this.

Gene Set Clustering based on Functional annotation (GeneSCF)

Answer 1

[bigmawen]

Pathview is actually quite flexible. It accepts different data formats (matrices, vectors), different data attributes (discrete, continuous, numeric, characters). It works with tens of different gene/compound IDs and ~3000 species. Please check the package tutorial and documentation:

http://www.bioconductor.org/packages/release/bioc/html/pathview.html

If you supply your data as it is, propably no program can figure out what that is. Most programs want you do basic data preparation and provide some information about the data.

Answer 2

[karl.stamm]

If you want to see nodes and edges on a graphical display, you need a way to define those connections.

Cytoscape is a good tool for viewing and manipulating networks. A plugin for Cytoscape called GenMapp-CS can automatically take networks from wikipathways.org and draw your gene sets on them. Its nice if you have a gene list with differential expression, because cytoscape can color each gene correspondingly.

I guess you want to find HSA00010 as a diagram, then highlight ALDH7A1 and BPGM on it. Iteration would make a diagram for every line of the file.

If you don't want to review thousands of pictures; what were you trying to do with this dataset?

Answer 3

[EagleEye]

Hi, try Cytoscape... It has various plugins to play with your data.