MNet Documents

MNet

MNet: a metabolic network-centered tool for interpreting metabolomic and transcriptomic data


Introduction

MNet features a built-in knowledgebase, dbMNet which is manually curated and provides information on metabolomics, including almost all currently available human metabolic interactions (gene-metabolite and metabolite-metabolite). Grounded in this knowledgebase, MNet offers one subnetwork analyser ( sNETlyser ) and three extended pathway analysers ( ePEAlyser , ePDAlyser , and eSEAlyser ) for user-input metabolomic and transcriptomic data.



Functions

Backend Functions

1. sNETlyser

The subnetwork analyser extends the dnet subnetwork algorithm to identify metabolite-gene and metabolite-metabolite subnetwork from metabolomics and transcriptomic data, capitalising our curated dbMNet metabolic network information.

2. ePEAlyser

The extended Pathway Enrichment Analyser. (A) Barplot of cluster1 enriched metabolic pathways corresponding to metabolites and genes. (B) Barplot of cluster2 enriched metabolic pathways corresponding to metabolites and genes.



3. ePDAlyser

The extended Pathway Differential Abundance analyser. The ePDA score captures the tendency for a pathway to exhibit increased or decreased levels of genes and metabolites that are statistically significant differences between two groups.

4. eSEAlyser

The extended pathway Set Enrichment Analyser, which aim to identify dysregulated metabolic pathways by considering both metabolites and genes.



Documents

1. MNet Web Server Manual

MNet Web Server Manual

2. MNet R Package References

MNet R Package References

Knowledgebase Update and Download

1. Knowledgebase Introduction:


The knowledgebase dbMNet is a freely available knowledgebase that attempts to consolidate information on all known genes and metabolites into a single resource. The knowledgebase includes two knowledgebases, dbNet and dbKEGG.

Knowledgebase dbKEGG, designed for extended pathway analysis sourced from KEGG database, encompasses 1,692 genes and 3,097 metabolites distributed across 84 metabolic pathways and 11 metabolic categories.

Knowledgebase dbNet, designed for metabolism-related subnetwork analysis sourced from KEGG, BiGG, Reactome, SMPDB and WikiPathways, encompasses a total of 54,593 metabolite-gene pairs and 51,719 metabolite-metabolite pairs were documented.

These pairs involve 3,964 genes, and 11,932 metabolites.

The source code for compiling the knowledgebase dbMNet is available here:

https://tuantuangui.github.io/MNet_manual/web-server-manual.html#construction-of-knowledgebase-dbmnet

2. Knowledgebase dbMNet V202411 can be downloaded here.


http://www.mnet4all.com/MNet/dbMNet/dbMNet-V202411.zip
Download

2.1 dbKEGG, designed for extended pathway analysis.



2.2 dbNet, designed for metabolism-related subnetwork analysis.


3. Knowledgebase History


3.1 Knowledgebase dbMNet V202404 can be downloaded here.


http://www.mnet4all.com/MNet/dbMNet/dbMNet-V202404.zip
Download

3.2 Knowledgebase dbMNet V202212 can be downloaded here.


http://www.mnet4all.com/MNet/dbMNet/dbMNet-V202212.zip
Download

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Nodes Data

Nodes Data: Nodes of subnetworks.

Edges Data

Edges Data: Edges of subnetworks.

A core metabolite-gene subnetwork can be downloaded as a PDF or JPEG file with specified width, height, and dpi setting.

Figure 1. Visualization of the identified optimal subnetwork that best explains the biological processes comparing two groups. The colors represent the logFC (logarithm of fold change) of genes and metabolites, with red and green indicating the logFC of genes, while yellow and blue represent the logFC of metabolites, indicating varying levels.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data: Sample's group information.

Nodes Data

Nodes Data: Nodes of subnetworks.

Edges Data

Edges Data: Edges of subnetworks.

Figure Download

A core metabolite-gene subnetwork can be downloaded as a PDF or JPEG file with specified width, height, and dpi setting.

Figure 1. Visualization of the identified optimal subnetwork that best explains the biological processes comparing two groups. The colors represent the logFC (logarithm of fold change) of genes and metabolites, with red and green indicating the logFC of genes, while yellow and blue represent the logFC of metabolites, indicating varying levels.

| Setting

Figure Download

| Data && Figure Preview

| Data Table

| Data Table

| Data Table

| Data Table

| Setting

Figure Download

| Data && Figure Preview

| Data Table

| Data Table

| Data Table

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Up ePEA Terms

Up ePEA Terms: Up-regulated pathways.

Down ePEA Terms

Down ePEA Terms: Down-regulated pathways.

Bar plot illustrating enriched pathways are available, and can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Extended pathway enrichment analysis. (A) Barplot of up-regulated metabolic pathways corresponding to metabolites and genes. (B) Barplot of down-regulated metabolic pathways corresponding to metabolites and genes.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data: Sample's group information.

Up ePEA Terms

Up ePEA Terms: Up-regulated pathways.

Down ePEA Terms

Down ePEA Terms: Down-regulated pathways.

Figure Download

Bar plot illustrating enriched pathways are available, and can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Extended pathway enrichment analysis. (A) Barplot of up-regulated metabolic pathways corresponding to metabolites and genes. (B) Barplot of down-regulated metabolic pathways corresponding to metabolites and genes.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

ePDA Terms

ePDA Terms: Result of ePDA analysis.

A DAscore plot captures the tendency for a pathway, and can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. ePDA score captures the tendency for a pathway to exhibit increased or decreased levels of genes and metabolites that are statistically significant differences between two groups.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data: Sample's group information.

ePDA Terms

ePDA Terms: Result of ePDA analysis.

Figure Download

A DAscore plot captures the tendency for a pathway, and can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. ePDA score captures the tendency for a pathway to exhibit increased or decreased levels of genes and metabolites that are statistically significant differences between two groups.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

eSEA Terms

eSEA Terms: Result of eSEA analysis.

Result of pathway set enrichment analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Extended pathway set enrichment analysis.

Result of interested pathway set enrichment analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 2. Extended interested pathway set enrichment analysis.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Gene Data (required, in .txt format): an interactive table for user input, with rows corresponding to gene symble and columns corresponding to samples.

Group Data: Sample's group information.

eSEA Terms

eSEA Terms: Result of eSEA analysis.

Figure Download

Result of pathway set enrichment analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Extended pathway set enrichment analysis.

Figure Download

Result of interested pathway set enrichment analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 2. Extended interested pathway set enrichment analysis.

| Setting

Figure Download

| Data && Figure Preview

| Data Table

| Data Table

| Data Table

| Setting

Figure Download

| Data && Figure Preview

| Data Table

| Data Table

| Data Table

| Setting

1. DATA UPLOAD:

Compound Name


Refmet Data

Refmet Data (required, in .txt format): Metabolites Refmet format.

| Setting

1. DATA UPLOAD:

Compound name


KEGGID Data

KEGGID Data (required, in .txt format): Metabolites KEGG format.

| Setting

1. DATA UPLOAD:

The compound name


Pathway Data

Pathway Data (required, in .txt format): Metabolites Pathway format.

| Setting

1. DATA UPLOAD:

The Compound KEGG ID


Pathway Data

Pathway Data (required, in .txt format): Metabolites Pathway format.

| Setting

1. DATA INPUT:

The pathway name or the pathway hsa ID


Gene Info Data

Gene Info Data (required, in .txt format): gene information table.

Compound Info Data

Compound Info Data (required, in .txt format): compound information table.

| Setting

1. DATA UPLOAD:

The pathway name


Pathway ID Data

Pathway ID Data (required, in .txt format): pathway ID format.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Diff Results

Diff Results: Result of differential metabolites analysis.

Result of volcano analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Differential metabolites and volcano plot.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data: Sample's group information.

Diff Results

Diff Results: Result of differential metabolites analysis.

Figure Download

Result of volcano analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Differential metabolites and volcano plot.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.

Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Boruta Results

Boruta Results: result of boruta analysis.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data: Sample's group information.

Boruta Results

Boruta Results: result of boruta analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.

Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Forest Results

Forest Results: result of forest analysis.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data: Sample's group information.

Forest Results

Forest Results: result of forest analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.

Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

XGBoost Results

XGBoost Results: result of xgboost analysis.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data: Sample's group information.

XGBoost Results

XGBoost Results: result of xgboost analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
Metabolite Data

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data

Group Data: Sample's group information.

Alpha Results

Alpha Results: result of lasso or elastic analysis.

Metabolite Data (required, in .txt format): An interactive table for user input, with rows corresponding to metabolites' KEGG IDs and columns corresponding to samples.

Group Data: Sample's group information.

Alpha Results

Alpha Results: result of lasso or elastic analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. FIGURE CANVAS:
Clinical Data

Clinical Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Result of time series analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Time series of clinical.

Clinical Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Figure Download

Result of time series analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Time series of clinical.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. FIGURE CANVAS:
Survival Data

Survival Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Result of survival analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Survival analysis.

Survival Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Figure Download

Result of survival analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Survival analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.



2. ANALYSIS PARAMETERS:
3. FIGURE CANVAS:
Survival Data

Survival Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Result of survival analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Survival analysis.

Survival Data (required, in .txt format): column contains the time, group, clinical index(such as ALT), low and high.

Figure Download

Result of survival analysis can be downloaded as a PDF or JPEG file with specified width, height, and dpi settings.

Figure 1. Survival analysis.

| Setting

1. DATA UPLOAD:

An example can be found in Demo, and click on ➕ to open it.

Survival Data

Survival Data (required, in .txt format): survival data.

Cox Result

Cox Result (required, in .txt format): cox analysis result.

Survival Data (required, in .txt format): survival data.

Cox Result

Cox Result (required, in .txt format): cox analysis result.