Pathview Web Server: user friendly pathway visualization and data integration

[bigmw]

Dear all,
We are happy to announce that Pathview Web server. It is online at http://pathview.uncc.edu/ since 2016. It was updated substantially in the last few months.

Pathview is a tool set we developed that maps, integrates and renders a large variety of biological data on molecular and genetic pathways, and produces interpretable graphs with publication quality.
Pathview web server extends the core functions of Pathview with:
-a simple intuitive graphical user interface
-fast and programmatic access through RESTful API
-complete pathway analysis workflow supporting multiple omics data and integrated analysis
-interactive and hyperlinked results graphs for better data interpretation
-most complete and up-to-date pathway data via regular database synchronization
-open access to all analyses and resources
-analysis history and data sharing via free registered user accounts
-complete online help and documentation
-multiple quick-start example analyses

Please try it, and let us know if you have any problem or comments. Thanks for your inputs in advance!

[bigmw]

For more info on Pathview:
R/BioC package:

http://bioconductor.org/packages/pathview/

Paper:

http://bioinformatics.oxfordjournals.org/content/29/14/1830.full

[littleseq]

I tried the example analysis, it worked fine. But when I tried my own data, there seemed to be some problem. I got an empty graph, and no colored nodes. Any idea on this?

[bigmw]

Not sure exactly what happened. But most likely, you did not specify the right data type, species or gene/compound ID type. Did you see any error message?

[littleseq]

Here is the error message:
Species and pathway id combination is not Valid/present at KEGG Or make sure your input gene and compound uploaded data is in the requested format

I checked the species and pathway IDs. They are indeed valid in kegg pathway website.

[bigmw]

If you are sure that your species is valid, you should check the gene/compound ID type or the input data type (gene or compound). If you specify these options wrong, you may get that error too.

[bigmw]

Pathview Web server was updated substantially in the last few months. Please check the main post above for details.
The server is online at http://pathview.uncc.edu/.