So what i did is using the blast2go to do the go enrichment analysis and for kegg i used the kaas kegg using the fatsa file of my genes.
How to get a collection mat file from kegg.
In a kgml file the pathway is represented as a graph.
But how can i download or get the pathway list.
Kegg dbschema file show indices false kegg dbinfo arguments file a connection or a character string naming the file to print to see the file argument of the cat function for the details.
Click on kegg pathway in the database column of the table near the top of the page.
1 12 2 which is the entry point to all of the kegg databases.
How would i retrieve the information for that particular drug.
The following link is graphical representation of metabolic pathways.
Our definition of flat file is not limited to text data.
Scientific name and the common name are always mapped to kegg code first.
This brings up a list of kegg s numerous pathways organized in a hierarchical manner fig.
Use show indices true to get them.
It also includes other types of data such as images for kegg pathways java graphics for genome maps and expression profiles and 3d graphics for protein structures.
Thanks for the info.
Species can be specified as either kegg code scientific name or the common name.
This is accomplished by treating a collection of html files as a database.
Character the file type s to be downloaded either kegg pathway data file xml or image file png.
Details kegg dbconn returns a connection.
Kegg pathway database is a collection of manually drawn pathway maps representing current knowledge on molecular interaction and reaction networks accompanied with kgml kegg pathway xml format files for automatic computational analyses and modeling of metabolic and signaling networks.
Show indices the create index statements are not shown by default.
Each map is manually drawn with in house software called kegsketch which generates the kgml file.
This brings up the kegg table of contents fig.
Ie am planning to develop the web application which would look up for the drug names in a article and the drug names detailed information should be linked to the kegg drug database.
Length of species should be either 1 or the same.
But from last few days it is not working.
I used pathway entry option before.
Kegg pathway database is a collection of manually drawn pathway maps representing current knowledge on molecular interaction and reaction networks accompanied with kgml kegg markup language files for automatic computational analyses and modelling of metabolic and signalling networks kanehisa et al 2010 pathways in kgml are represented as graph objects with entry elements.
Default include both types.
Plz help me out.
