Questions tagged [kegg]
The kegg tag has no usage guidance.
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enrichKegg arbitrarily excluding certain genes from gene set during analysis
I'm using the R-package enrichKEGG to perform an enrichment analysis on a vector of genes. As output I get a list of pathways containing some number of the genes in my vector. In the results there is ...
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How to only enrich sensible GO and KEGG terms?
I'm thinking of analyzing enriched pathways using KEGG and GO databases on de-novo assembled transcripts using clusterProfiler 4.0. After annotating them with ...
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Should I include unannotated transcripts in a pathway enrichment analysis of a de-novo assembled transcriptome?
I'm trying to perform an enrichment analysis on a set of Transcripts assembled de-novo, using a GSEA like method on KEGG and GO. The set contains annotated and unannotated transcripts. My question is:
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KEGG IDs and gene IDs going unrecognized in Cytoscape metscape software
I'm new to using metscape and am having some trouble with entering my compound IDs and gene IDs into the system. When I enter my compound IDs as KEGG IDs, around a quarter of my data goes unrecognized ...
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Gene set enrichment ontology analysis issue
I have been dealing with this problem for the past 48 hrs. I do not know what is it, which prevents the function from assessing the parameters it gets passed.
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MEGA11 gives the error "stop codons are found in the translated sequences", even though there are not!
I am using MEGA11 MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , Mol. Biol. Evol. 38(7):3022–3027 to align protein coding sequences that I downloaded from KEGG database. I am ...
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
I am working on using WGCNA for a bulk RNA-seq experiment. I have three experimental conditions (control, treatment 1, and treatment 2) and have a total sample size of 18 (6 per group). Using the ...
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122
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How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment)
With HUMAnN3, I got the result of the KEGG KO annotation (by humann_regroup_table:humann_regroup_table --input hmp_subset_genefamilies.tsv --groups uniref90_ko --output ...
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Refactoring pandas using an iterator via chunksize
This question was also asked on Stack Overflow
Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops.
I am looking for advice on using ...
M__♦
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How to extract sequences of a specific gene from genomes, with genomes' .fna, .gff and results from KofamScan?
I am trying to do alignment among orthologs and paralogs of a gene but I encountered some problems. I have came up with a workflow, but the sequences I extracted are not correct. They are of hugely ...
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COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results
I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the ...
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eggNOG: DNA-DNA or protein-protein orthologue identification?
I'm trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues.
Background eggNOG is ...
M__♦
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99
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Analysis of 4665 proteins in String database
Background I have a data set of 4665 proteins from Phytophthora cactorum and want to analyze them in the String database as other database does not have Phytophthora cactorum for GO or KEGG analysis. ...
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83
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KEGG retrieve hierarchy for organism in biopython
I want to obtain a direct graph from KEGG as well as the genes present in a single term. While it is pretty easy to get list of genes/compounds that are part of a specific category, I am kinda stucked ...
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Naming conventions for kegg nodes with multiple genes
So I'm downloading XML files from Kegg using BioConductor and and I'm running into a problem. If we look at HIF-1 signaling pathway we see the node growth factor (GF) on the left hand side, we can ...
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How to annotate list of proteins with KEGG orthology groups?
I've got a list of proteins, complete with Uniprot IDs (for some of them) and gene names. I'd like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column ...
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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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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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163
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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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143
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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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252
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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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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 ...
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222
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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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580
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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 ...
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95
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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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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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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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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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119
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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 ...
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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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