Questions tagged [kegg]

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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
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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: <...