3mcor

Metabolomics Pathway Deregulation Matrix Generation

This tool transfers metabolic intensity/concentration matrix to pathway deregulation/activity matrix with the support of KEGG. The R package Lilikoi and Pathifier were used [1, 2]. The input and output matrices have the same number of samples. The resulting pathway matrix can be input into 3MCor directly for further correlation analysis.

Attach Table

Input files of the metabolic intensity/concentration matrix (.csv) consists of: sample name (at the first column), groups information (at the second column), metabolites id in the KEGG(at the first raw). The sample is as follows:

	Label	C00099	C00300	C01026	C00334
sample1	human	20.27	1.265	3.34	4.65
sample2	human	30.54	2.53	10.46	12.18
sample3	human	30.52	10.56	10.41	10.82
sample4	pig	40.63	20.86	10.62	20.68
sample5	pig	60.14	9.61	9.42	40.65
sample6	pig	44.94	6.91	69.26	64.34

The result is as follows:

	Alanine Metabolism	Bile Acid Biosynthesis	Cysteine Metabolism	Demeclocycline Action Pathway
sample1	0.846	0.778	0.77	0.801
sample2	0.894	0.853	0.468	0.718
sample3	0.884	0.0395	0.041	0.782
sample4	0.673	0.866	0.672	0.068
sample5	0.164	0.681	0.039	0.065
sample6	0.594	0.901	0.026	0.384

.csv file. You must upload of the metabolome data for further analysis. Please see the example for detail.

Demo data

[1] Al-Akwaa FM, Yunits B, Huang S, Alhajaji H, Garmire LX. Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data. Gigascience. 2018 Dec 1;7(12):giy136. doi: 10.1093/gigascience/giy136. PMID: 30535020; PMCID: PMC6290884. [2] Drier Y, Sheffer M, Domany E. Pathway-based personalized analysis of cancer. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6388-93. doi: 10.1073/pnas.1219651110. Epub 2013 Apr 1. PMID: 23547110; PMCID: PMC3631698.