Retrieve list of human Kegg pathway identifiers for Environmental Information Processing

Question

[avari]

Dear experts,

I wish to retrieve a list of human Kegg pathway identifiers for several general biological 'themes' from the Kegg website (such as all environmental signal processing pathway ids) but as I am new to bioinformatics I am unsure how best to do this. I want to go on to use this list of identifiers in the clusterProfiler package in R. I have looked into the available Bioconductor packages such as Kegg.db and KEGGREST but it is not clear to me from the documentation whether I can use them for this purpose and I don't want to invest my time in learning how to use the packages if/they are outdated or there is simpler way to do this.

Any suggestions would be very welcome!

Thanks,
Luanna

[Na Sed]

I have already worked with a package, called "graphite". It includes kegg pathways and their ids. Of course the goal of this package is not providing name and id of kegg pathways, but you can use it to find id of kegg pathways as well.

[avari]

Great, thanks for the recommendation, I will give it a try!

[avari]

Hi, just a quick update. The graphite package certainly looks promising, but I wondered if you could tell me which function you used to extract the pathways? I already have a list of human Kegg pathways, so I am looking to retrieve only those involved in 'environmental information processing' but I couldn't work out how to do that. Thanks again!

[Na Sed]

'graphite' just includes pathway names and their identifiers.

It does not include any categorization of pathways. So you must determine the name of desired pathways, then you can get their identifiers using graphite package.

Answer 1

[theobroma22]

Is this what your looking for? http://www.kegg.jp/kegg/pathway.html#environmental

3. Environmental Information Processing

3.1 Membrane transport
02010ABC transporters
02060Phosphotransferase system (PTS)
03070Bacterial secretion system

3.2 Signal Transduction
02020Two-component system
04014Ras signaling pathway
04015Rap1 signaling pathway
04010MAPK signaling pathway04013MAPK signaling pathway - fly04016MAPK signaling pathway - plant04011MAPK signaling pathway - yeast04012ErbB signaling pathway04310Wnt signaling pathway04330Notch signaling pathway04340Hedgehog signaling pathway04341Hedgehog signaling pathway - fly04350TGF-beta signaling pathway04390Hippo signaling pathway04391Hippo signaling pathway - fly04392Hippo signaling pathway - multiple species04370VEGF signaling pathway04371Apelin signaling pathway04630Jak-STAT signaling pathway04064NF-kappa B signaling pathway04668TNF signaling pathway04066HIF-1 signaling pathway04068FoxO signaling pathway04020Calcium signaling pathway04070Phosphatidylinositol signaling system04072Phospholipase D signaling pathway04071Sphingolipid signaling pathway04024cAMP signaling pathway04022cGMP-PKG signaling pathway04151PI3K-Akt signaling pathway04152AMPK signaling pathway04150mTOR signaling pathway04075Plant hormone signal transduction

3.3 Signaling molecules and interaction
04080 Neuroactive ligand-receptor interaction
04060Cytokine-cytokine receptor interaction
04512ECM-receptor interaction
04514Cell adhesion molecules (CAMs)