Questions tagged [kegg]

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What genes are driving a certain pathway

I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway. ...
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DAVID returning invalid KEGG pathways in gene enrichment analysis

I'm using the latest version of DAVID Knowledgebase (v2021q4, Available at https://david-d.ncifcrf.gov) for enrichment of a set of genes that I have. Using the ...
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How to get KEGG pathway names from a list of 'ko' IDs?

I have a list of ko IDs from which I want to get the pathway names. How can I get that? I have tried this link, but it does not give me any result. What to do? ...
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2 answers
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Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
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After KEGG and GO analysis, how to make tables+phylogenetic trees

hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header : for GO ...
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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 ...
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3 votes
1 answer
92 views

How to load output from the kegg API in biopython into a pandas dataframe?

Biopython provides a (bit unintuitive) API to access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). I am trying to make use of it, but the output is quite unhandy as a string. What is the best ...
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28 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 ...
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61 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 such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
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124 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 ...
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3 answers
398 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 ...
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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 ...
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1 answer
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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 ...
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  • 171
2 votes
2 answers
594 views

How to interconvert InChI and InChIKey?

I would like to retrieve IDs from several databases using InChI as an input, e.g. ...
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3 votes
1 answer
370 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: ...
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2 answers
103 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 ...
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9 votes
1 answer
199 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: <...
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