How to make a KEGG map from humann2 pathways

Microbial community profiling HUMAnN
1

Hi,
I got the metabolic pathways through humann2 but i am interested to make a map of all important pathways, please can someone suggest me, how i can make it as an attached image. Humann2 pathways doesn’t have KEGG IDs and but have PWY numbers, i don’t know how i can use them to make a map.

Thanks,
Khem

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2

The pathways provided by HUMAnN 2.0 are from the MetaCyc pathway database, so they will not work with KEGG’s visualization system. MetaCyc has its own visualization system called “Pathway Collages”:

https://metacyc.org/pathway-collage-info

Perhaps this will accomplish what you need?

3

Thanks Eric, This is great.
One additional question:
My lab can get the KEGG subscription and i was thinking to use humann2 with custom database option but do i need to make any changes in KEGG database format? if yes, please can you suggest or share the procedure in order to use with humann2?

Thanks,
Khem

4

We have some recommendations about using the legacy (HUMAnN 1.0) KEGG databases with HUMAnN 2.0 here:

Perhaps you could adapt them to work with the updated KEGG database?

5

Sorry if My question sounds stupid,
I don’t have any idea about updated KEGG database (subscription based) format n all,
Do you know by any chance, if i adapt the method from legacy HUmann1-KEGG for updated KEGG one, will it work or is there anything else needs to be done?
Reason i am asking, i do not want to waste 2000$ for subscription of my PI, if i wont be able to work on.
Thanks,
Khem
Thanks,
Khem

6

Apologies - I read your previous post as saying you already have the subscription. I can’t make any guarantees about the subscription-based KEGG since I don’t have access to it myself for testing.

7

Okay Thank you so much Eric for your kind support,
I will ask this question again in the forum as a separate topic, i hope someone has experience on it,

Khem

8

Dear Khem, Dear Eric,

I am also interested in visualizing humann2 output in terms of ‘patway mapping’ and identify differences between groups in terms of presence, abundance or expression of pathways or genes (I am anaylising paires metegenomes / metatranscriptomes).
For instance, how could I map and visualize differntially abundant features (identified with Maaslin2) in a braoder metabolic context?

Thanks a ton.

Florentin

1 Like
9

Dear Eric,

I am interested in displaying MEtaCyc pathways/gene families similarly to what you suggested using patway-collage.

My goal would be to visualize pathways/gene families in a metabolic context as well as contributing species (RNA/DNA ratio - I have paired metagenomic and metatranscriptomic samples). This was achieved using other tools as metaphlan/humann here.

  • It should be feasible with humann3 outputs, right?
  • Have you already achieve this can of visualisation? using metacyc - pathway-collage?
  • Would you suggest another approach/ tool?

Many thanks.

Florentin

10

any help to put genes and species contributing to those in a pathway context would be very much appreciated!