Questions tagged [kegg]
The kegg tag has no usage guidance.
17
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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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- 317
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32
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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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42
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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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44
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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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- 11
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110
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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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92
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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
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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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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 ...
- 21
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124
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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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398
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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 ...
- 4,622
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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 ...
- 121
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46
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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 ...
- 171
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594
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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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370
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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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103
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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 ...
- 1,347
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199
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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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