Questions tagged [kegg]
The kegg tag has no usage guidance.
12
questions
0
votes
1answer
56 views
How to represent pathways as mathematical graphs?
I would like to construct a mathematical graph: $G = (E,V, w(E))$ a graph with vertices, edges with weight on them based on a KEGG pathway.
Is there a way to do that with existing tools? If not I ...
2
votes
0answers
20 views
How to load output from the kegg API in biopython into a pandas dataframe?
Biopython provides a (bit unintuitive) API to access KEGG. I am trying to make use of it, but the output is quite unhandy as a string. What is the best way to parse the data into a ...
1
vote
1answer
18 views
How to map selected genes to Metabolic pathway Maps
I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
2
votes
0answers
39 views
Number of reactions per metabolic pathway
What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database (kegg, metacyc,reactome..) is more helpful/reliable for ...
1
vote
0answers
86 views
Downloading full search results from BlastKOALA?
I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: https://www.kegg.jp/blastkoala/
When you get results, there are links for ...
5
votes
3answers
209 views
KEGG FTP vs KEGG API
I was reading the KEGG plea and I found that it doesn't forbid using the KEGG API. Then, what is in the FTP server license for personal use/academic use that it is not covered by the API?
Or I could ...
2
votes
0answers
70 views
Locate KEGG/Reactome pathways in user defined network
I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways ...
2
votes
1answer
44 views
AND or OR gene - protein logical relation in KEGG
How do I know if it is a AND or OR relationship between genes associated with the same enzyme in KEGG? E.g., for EC:1.6.1.2 (http://www.genome.jp/dbget-bin/www_bget?ec:1.6.1.2) does the bacterium ...
1
vote
2answers
247 views
How to interconvert InChI and InChIKey?
I would like to retrieve IDs from several databases using InChI as an input, e.g.
...
3
votes
1answer
221 views
How to retrieve InChI key for KEGG compound?
I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices).
One could do it via ChEBI like this:
...
0
votes
2answers
96 views
How can I find the relevant pathway map from gene-gene or protein-protein interaction list? [closed]
I have some difficulties to understand/interpret the pathway map and how a gene-gene interaction list or DNA sequencing can map into pathways.
In addition what's the difference between MARK/ERK ...
9
votes
1answer
184 views
How to retrieve logical expressions (KO based) for reactions from KEGG?
The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as:
<...
