Question: (Closed) Cannot Color Human Pathways In Kegg
1
gravatar for Ashis
7.6 years ago by
Ashis90
Baltimore, USA
Ashis90 wrote:

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

pathway kegg • 2.4k views
ADD COMMENTlink modified 7.1 years ago by Biostar ♦♦ 20 • written 7.6 years ago by Ashis90

This question can be closed, it was related to a temporary problem in KEGG.

ADD REPLYlink written 7.1 years ago by Giovanni M Dall'Olio27k
2
gravatar for Giovanni M Dall'Olio
7.6 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

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.

ADD COMMENTlink written 7.6 years ago by Giovanni M Dall'Olio27k
1
gravatar for Heather Vincent
7.6 years ago by
Manchester, UK
Heather Vincent160 wrote:

Cytoscape (http://www.cytoscape.org/) is useful for visualising data of this type.

ADD COMMENTlink written 7.6 years ago by Heather Vincent160
0
gravatar for Ashis
7.6 years ago by
Ashis90
Baltimore, USA
Ashis90 wrote:

Hi Heather Vincent and Giovanni M Dall'Olio,

Thank you both of you. I have sent my query to the support.

ADD COMMENTlink written 7.6 years ago by Ashis90
1

KEGG support is really wonderful. They have already answered my question. According them, it was a temporary phenomenon due to their mistake. The problem has already been fixed.

ADD REPLYlink written 7.6 years ago by Ashis90
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