MetaboAnalyst Pathway analyses issue

[Rada90]

Dear all,
thanks for hearing me out. I’m new to the topic (metabolomics) and I’m trying to use MetaboAnalyst to run some Analyses. I managed to run correctly a statistical analyses however I’m finding difficulties in running a complete pathway analyses. I’ve got my dataset and i managed to look at the HMDB name of my metabolites of interest. However as i insert them as HMDB ID and proceed the software couldn’t find any correspondence nor hmdb name (even if they are already there) not Kegg ID. I attach here a screenshot to show what the problem is. Am I doing something wrong or it is suppose to be like this?
Thanks again,
Davide

[jeff.xia]

Please read and follow our post guide

[Rada90]

Dear Jeff, apologies for not following the guide. I’ll share here the issue and attach here the dataset and a description of the step i take.
step 1. select “pathway analyses”;
step2. module “compound list” i attach the HMDB name of my metabolites and select the input type “HMDB ID”;
step 3. in the next page i’ve got no results so I can not procede with the analyses. It looks like there are no metabolites in the database.

Here the (short) compound list:
HMDB0007874
HMDB0013444
HMDB0240633
HMDB0007972
HMDB0048098
HMDB0013450
HMDB0013405
HMDB0004978
HMDB0009914
HMDB0007982
HMDB0011295
HMDB0008086
HMDB0009069
HMDB0007946
HMDB0054358
HMDB0009229
HMDB0051548
HMDB0007921

Thank you very much for the help.

[Qiang]

Hi Rada,

Thanks for sharing the compound list with us. We quickly checked these compounds and noticed they are all lipids. For Pathway analysis module, MetaboAnalyst would only recognize compounds which are actually involved in metabolic pathways. All others (e.g. lipids) will not be included (and recognized) because they are not contributing to the pathway analysis. For your case, if you really want to analyze those lipids, you should try to use Enrichment Analysis module, which offers specific lipids datasets. Or if you are interested in these compounds themselves, you can try to use Compound ID conversion function to check them.

All the bests,
Zhiqiang

[Rada90]

Hi Qiang,
thanks for the quick and fast reply. Apologies for the stupid question. I’ll do the enrichment analyses as you suggested. Sorry for taking your time but i’m new to the topic and I would like to extend my knowledge in the field, can you please suggest a book to understand a little bit more about the topic?

Thanks again
Davide