Analysis report
Xiaotao Shen, Zhengjiang Zhu
2017-08-21
(1) INTRODUCTION
MetDNA is used for metabolite annotation and dysregulated network analysis of untargeted metabolomics.
(2) PARAMETERS
Table 1: The parameter setting of this analysis
| Patameter | Value | Meaning |
|---|---|---|
| mz.tol | 25 | The tolerance of m/z (ppm) |
| rt.tol.for.ms1.ms2.match | 10 | The tolerance of RT for MS1 data and MS2 data matching (second) |
| polarity | positive | The acquisition mode of data (positive or negative) |
| column | hilic | The LC system (hilic or rp) |
| ce | 30 | The collision energy of MS2 data acquisition |
| threads | 3 | The number of thread |
| rt.tol1 | 3 | The tolerance of RT for isotope and adduct peak annotation (second) |
| rt.tol2 | 30 | The tolerance of RT for metabolite annotation (%) |
| dp.tol | 0.5 | The tolerance of dop product in MRN annotation |
| group | W03,W30 | The group of you data analysis |
| uni.test | t | The univariate statistics method |
| correct | TRUE | Adjust p value or not |
| p.cutoff | 0.01 | The cutoff of p values |
| species | hsa | The species of your data |
(3) SAMPLE INFORMATION
Figure 1: Peak distribution
(4) METABOLITE ANNOTATION
The metabolite annotation is based on metabolic reaction network.
Figure 2: Recursive annotation and redundancy removal
Confidence level (from grade 1 to grad 4) is assigned to each metabolie.
Figure 3: The confidence levles of metabolites
(5) Dysregulated network analysis
Dysregulated peaks (according to pvalues) are used to identify dysregulated modules. The dysregulated modules with p values less than 0.05 are combined as dysregulated network. Metabolite set analysis (MSEA) is used to annotate functions of each module. The MSEA result for each module can be found in /Dysregulated_network_analysis_result_POS/module_information/Module_MSE analysis.
Figure 4: Summary of module information
Table 2: The information of dysregualted modules. The detailed information can be got from module.result.csv in /Dysregulated_network_analysis_result_POS/module_information
| Module name | Module impact | p value | Module size | Overlap (%) | Function annotation (enrichment pathway) |
|---|---|---|---|---|---|
| module1 | 0.7952381 | 0.00004 | 64 | 79.68750 | Galactose metabolism;Starch and sucrose metabolism |
| module2 | 0.4108527 | 0.00328 | 84 | 50.00000 | Pentose phosphate pathway;Purine metabolism;Galactose metabolism;Pentose and glucuronate interconversions |
| module3 | 0.4509804 | 0.01643 | 32 | 59.37500 | Caffeine metabolism;One carbon pool by folate;Folate biosynthesis |
| module4 | 0.4677419 | 0.04372 | 40 | 47.50000 | Synthesis and degradation of ketone bodies;Glyoxylate and dicarboxylate metabolism;Valine, leucine and isoleucine degradation;Butanoate metabolism;Phenylalanine metabolism;Propanoate metabolism;Pyruvate metabolism;Citrate cycle (TCA cycle);Fatty acid degradation |
| module5 | 0.5400000 | 0.11263 | 17 | 58.82353 | Cysteine and methionine metabolism;Glycine, serine and threonine metabolism;Sulfur metabolism |
Figure 5: Summary of dysregulated network information
Table 3: The information of dysregualted networks. The detailed information can be got from dysregulated.network.MSEA.csv in /Dysregulated_network_analysis_result_POS/pathway_information.
| Pathway name | p value | p value(adjusted) | Pathway size | Overlap (%) |
|---|---|---|---|---|
| Galactose metabolism | 0.0000000 | 0.0000000 | 46 | 39.13043 |
| Pentose phosphate pathway | 0.0000023 | 0.0000934 | 35 | 28.57143 |
| Starch and sucrose metabolism | 0.0002193 | 0.0059204 | 37 | 21.62162 |
| One carbon pool by folate | 0.0004713 | 0.0095429 | 9 | 44.44444 |
| Caffeine metabolism | 0.0022558 | 0.0365434 | 21 | 23.80952 |