A website for metabolomics data analysis and mining Sara Cardoso 1, - - PowerPoint PPT Presentation

WebSpecmine: A website for metabolomics data analysis and mining

Sara Cardoso1,*, Telma Afonso1, Marcelo Maraschin2, and Miguel Rocha1,*

1 CEB - Centre Biological Engineering, University of Minho, Campus of Gualtar,

Braga, Portugal;

2 Plant Morphogenesis and Biochemistry Laboratory

, Federal University of Santa Catarina, Florianpolis, SC, Brazil.

* Corresponding authors: saracardoso501@gmail.com; mrocha@di.uminho.pt

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WebSpecmine: A website for metabolomics data analysis and mining

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Introduction

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Metabolomics

✓ Analysingmetabolomics data correctly and efficiently is nowadays very important in biological and biomedical research. A website to perform metabolomicsdata analysisis an importantasset Most people that want to perform this analysismay not have the programming skills needed However

Introduction

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Some of the Existing Websites

Covered Techniques

LC/GC-MS Raw Spectra LC/GC-MS Raw Spectra LC/GC-MS Peak Lists NMR Peak Lists Metabolites' Concentrations (Quantitative Data)

Univariate Analysis

T-Test; ANOVA; Fold Change T-Test; ANOVA; Non-Parametric Tests;

Multivariate Analysis

PCA; Clustering; Machine Learning (only PLS-DA); Feature Selection (only Random Forests and SVM) PCA; Clustering; Machine Learning (only LDA, PLS-DA and Random Forests)

Other Features

Correlation Analysis; Metabolite Identification (only for MS); Pathway Analysis Metabolite Identification; Pathway Analysis; User Account

Introduction

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What is missing in the existing websites?

A wide variety of techniques and data formats supported SpectralData (Raman, UV-Vis and IR) is missing A wide variety of pre-processing methods Mostly just normalization, scaling, missing values treatment A wide variety of analysis methods There should be more model options for machine learning, for example Flexible Pipeline Most of the time, users have to follow a strict pipeline User Account So that data and results can be stored and shared

What was our main goal, then?

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SOLUTION: ✓ Create an easy-to-use and freely available website that provides a wide variety of methods and data types for analysis, and ways to store and share metabolomics data and the results generated.

WebSpecmine: overview

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Metabolomicsdata Supported ✓ NMR ✓ LC/GC-MS ✓ Infrared, UV-Visible, and Raman Spectra ✓ ConcentrationsData(QuantitativeData) Metabolomicsdata Analysis Available ✓ UnivariateStatistical Analysis ✓ Unsupervised MultivariateStatisticalAnalysis ✓ Supervised MultivariateStatistical Analysis ✓ MetaboliteIdentification ✓ Pathway Analysis Data Pre-Processing User Account ✓ Store data and results privately ✓ Share data across users Tutorials and User Guide

WebSpecmine: Supported data

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LC/GC-MS

Raw Spectra Data Formats ✓ .mzData ✓ .mzXML ✓ .netDF Peak Lists Data Formats ✓ CSV ✓ TSV

WebSpecmine: Supported data

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NMR

Raw Spectra Data Formats ✓ BRUKER ✓ VARIAN Peak Lists Data Formats ✓ CSV ✓ TSV

WebSpecmine: Supported data

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Spectral Data: Raman, IR and UV-Vis

Spectra Data Formats ✓ CSV ✓ (J)DX ✓ SPC ✓ MS EXCEL (.xlsx)

WebSpecmine: Supported data

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✓ CSV/TSV File:

Concentrations (Quantitative) Data

Metabolites Names or Identifiers Samples' Names Concentrations values of each metabolite in each sample

WebSpecmine: Supported data

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Metadata

✓ CSV/TSV File: ✓ All types of data should have a metadata file associated

Samples' Names Names of the metadata classes Metadata values for each metadata class in each sample

WebSpecmine: User Account

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Why a User Account?

✓ Main website functionalitiesare accessible without a user account ✓ But you will have to create an account if you want to:

• Save and Share data and results
• Leave an analysisin 'stand-by'

WebSpecmine: User Account

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Creationof a User Account

To have one, users have to send an email, asking to create an account, and an email with the credentials will be sent as soon as possible. Email: webspecmine@gmail.com

WebSpecmine: User Account

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Data Projects: What is?

A project is a study, or group of studies, which contains the data and metadatafor each study, as well as reports from the results obtained Projects can be: Private Public

WebSpecmine: User Account

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Your Projects

The projects stored in an account are accessible through My Projects sidebar tab

WebSpecmine: User Account

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Public Projects

Everyone that accesses the website can see all public projects, at the Public Projects sidebar tab

WebSpecmine: User Account

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Public Projects

Everyone that accesses the website can see all public projects, at Public Projects sidebar tab To analyse a public project, you would have to copy it to your account and analyse it from there, so that the original project is not compromised.

WebSpecmine: User Account

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Workspace: Users can leave their analysis in 'stand-by' and continue later

Users can leave an analysis at any time, by saving the workspace, and continue next time

WebSpecmine: Select Data for Analysis

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For Logged In Users 1

Select the Project, the data folder from that project where the data to analyse is, and the metadata file from that project that corresponds to the data selected

WebSpecmine: Select Data for Analysis

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For Logged In Users 1 2

Set the options required to correctly read the data and metadata files

WebSpecmine: Select Data for Analysis

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For Logged In Users 1 2 3

After finishing the setting of data and metadataoptions, the user can submit the data for analysis

WebSpecmine: Select Data for Analysis

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For Logged Out Users

✓ The Procedure is similar, but the data files and metadata files have to be submitted, as they are not stored in the website. ✓ The data submitted will only be temporarilystored, while the analysis is in action.

Once the user selects the data, the data analysis pages will be accessible

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WebSpecmine: Data Visualization

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The website provides a way to visualize the data

WebSpecmine: Data Visualization

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Data Summary

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WebSpecmine: Data Visualization

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Data and Metadata Tables

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WebSpecmine: Data Visualization

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Samples' and Variables' Statistics

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WebSpecmine: Data Visualization

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Boxplots of the Variables

2 3 4 5

WebSpecmine: Data Visualization

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Plot for Peaks Data

2 3 4 5 6

WebSpecmine: Data Visualization

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Plot for Spectra

2 3 4 5 6

WebSpecmine: Pre-Processing

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1

The website provides a wide variety of pre-processing methods, that can be performed in the desired order

WebSpecmine: Pre-Processing

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1

Methods that are availablefor all types of data

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WebSpecmine: Pre-Processing

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1

Methods that are availablefor all types of data

2

WebSpecmine: Pre-Processing

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1

Methods that are availablefor all types of data

2

WebSpecmine: Pre-Processing

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Methods only for spectral data

2 3

WebSpecmine: Pre-Processing

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Method only for NMR Spectra

2 3 4

WebSpecmine: Pre-Processing

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1

After processing the data, a name to the new dataset has to be given

2 3 4 5

To perform an analysis on the new dataset, the user will have to choose it

• n the sidebar panel

WebSpecmine: Data Analysis

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WebSpecmine: Data Analysis

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Univariate Analysis

Example for T-Test

Analysis options for a T-Test

WebSpecmine: Data Analysis

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Univariate Analysis

Example for T-Test

Types of results available for this type of analysis: numerical results

WebSpecmine: Data Analysis

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Univariate Analysis

Example for T-Test

Types of results available for this type of analysis: plot

WebSpecmine: Data Analysis

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Univariate Analysis

Other Analysis

There are other Univariate Analysis methods available The types of results available for each analysis is similar to those showed for T-Test

WebSpecmine: Data Analysis

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Principal Components Analysis (PCA)

Analysis options for both normal and robust PCAs

WebSpecmine: Data Analysis

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Principal Components Analysis (PCA)

Types of results available for this type of analysis: numerical results

WebSpecmine: Data Analysis

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Principal Components Analysis (PCA)

Types of results available for this type of analysis: plot results

WebSpecmine: Data Analysis

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Principal Components Analysis (PCA)

Types of results available for this type

• f analysis: plot results

Hierarchical Clustering

WebSpecmine: Data Analysis

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Clustering Analysis

Analysis options

WebSpecmine: Data Analysis

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Clustering Analysis

Hierarchical Clustering

Types of results available for this type of analysis

K-Means Clustering

WebSpecmine: Data Analysis

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Clustering Analysis

Analysis options

WebSpecmine: Data Analysis

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Clustering Analysis

K-Means Clustering

Types of results available for this type of analysis

WebSpecmine: Data Analysis

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Machine Learning

Train Models

Analysis options

WebSpecmine: Data Analysis

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Machine Learning

Train Models

Analysis options

Available models:

• PLS
• Decision Tree
• Rule-Based Classifier
• SVMs with Linear Kernel
• Random Forests
• Linear Discriminant Analysis
• Neural Networks

WebSpecmine: Data Analysis

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Machine Learning

Train Models

Types of results available for this type of analysis

WebSpecmine: Data Analysis

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Machine Learning

Predict New Samples

Analysis options

WebSpecmine: Data Analysis

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Machine Learning

Predict New Samples

Types of results available for this type of analysis

WebSpecmine: Data Analysis

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Feature Selection

Analysis options

WebSpecmine: Data Analysis

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Feature Selection

Types of results available for this type of analysis

WebSpecmine: Data Analysis

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Regression Analysis

Regression Analysis

Analysis options

WebSpecmine: Data Analysis

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Regression Analysis

RegressionAnalysis

Types of results available for this type of analysis: numerical results

WebSpecmine: Data Analysis

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Regression Analysis

Regression Analysis

Types of results available for this type of analysis: plot results

WebSpecmine: Data Analysis

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Regression Analysis

Correlation Analysis

Analysis options

WebSpecmine: Data Analysis

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Regression Analysis

CorrelationAnalysis

Types of results available for this type of analysis: numerical results

WebSpecmine: Data Analysis

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Regression Analysis

Correlation Analysis

Types of results available for this type of analysis: plot results

WebSpecmine: Data Analysis

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Metabolite Identification

LC-MS Data

Analysis options

WebSpecmine: Data Analysis

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Metabolite Identification

LC-MS Data

Results available for this type of analysis

WebSpecmine: Data Analysis

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Metabolite Identification

NMR Data

Analysis options

WebSpecmine: Data Analysis

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Metabolite Identification

NMR Data

Results available for this type of analysis

WebSpecmine: Data Analysis

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Pathway Analysis

Analysis options

WebSpecmine: Data Analysis

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Pathway Analysis

Results available for this type of analysis

WebSpecmine: Analysis of MetaboLights Studies

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You can see information on some of the MetaboLights studies

WebSpecmine: Analysis of MetaboLights Studies

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You can see detailed information on the protocol and metadata information on each assay

WebSpecmine: Analysis of MetaboLights Studies

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You can download the data and metadata of an assay into your private account and analyse it

Conclusions

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✓ We were able to create an easy-to-use and freely availablewebsite with many advantages:

▪ Wide variety of techniques and data formats supported ▪ Wide variety of pre-processing methods ▪ Wide variety of analysis methods ▪ User Account ▪ Flexible Pipeline

✓ However, more analyses could be added, to add more biologicalmeaningto data, such as:

▪ Enrichment Analysis ▪ Biomarker Analysis

For More Detailed Information ...

Website Link: https://webspecmine.bio.di.uminho.pt/ We have Tutorials and a complete User Guide at the ?Help page. We have a troubleshooting window, from where the users can report any problems and see the problems already encountered, but still being solved.

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Acknowledgments

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Christopher Costa, for being the main developer of the specmine R package