Hi,
I am using the human pathways from KEGG for my research. I need to use the search&color pathway tool frequently to color a set of genes (I have the KEGG Gene IDs). It was working just fine for me. However, from this morning (4 April 2013), I found that the SearchAgainst dropdown box no more contains the entry "Homo Sapiens Pathway (hsa)". Notably, the 2nd example beside the big input textbox does not work. (Input: 7167 red,blue). Can anyone please suggest me any alternative option?
Thanks in Advance.
Regards,
Ashis
3 answers
Unfortunately your problem is complicated by the fact that the KEGG's ftp has recently become a paid service. This means that you can find few tools that can query Kegg's data and produce images similar to what you have shown. Moreover, you will probably have to pay to use Kegg's data programmatically.
Option 1: contact KEGG's support
Kegg has a very wonderful support service. They usually answer within a few days, and they are very kind. You should just write them using the Support Form, tell them that you made a great use of their search&color tool, and ask them why they removed that option.
Option 2: use another database
As Heather already commented, Cytoscape has a very good functionality to automatically retrieve pathway data from other databases (Like Reactome and WikiPathways), and plugins to search nodes and color them.
Cytoscape (http://www.cytoscape.org/) is useful for visualising data of this type.
Log in to answer this question.
This question can be closed, it was related to a temporary problem in KEGG.