This is the fifth module in the 2016 Informatics and Statistics for Metabolomics workshop hosted by the Canadian Bioinformatics Workshops. This lecture is by David Wishart from the University of Alberta.

How it Begins by Kevin MacLeod is licensed under a Creative Commons Attribution license (https://creativecommons.org/licenses/...)

Source: http://incompetech.com/music/royalty-...

Artist: http://incompetech.com/

Table of Contents:

00:10 -

00:56 - Learning Objectives

01:15 - A Typical Metabolomics Experiment

03:16 - 2 Routes to Metabolomics

03:31 - Metabolomics Data Workflow

05:11 - Data Integrity/Quality

06:46 - Data/Spectral Alignment

07:28 - Binning (3000 pts to 14 bins)

07:53 - Data Normalization/Scaling

09:40 - Data Normalization/Scaling

10:20 - Data QC, Outlier Removal & Data Reduction

12:08 - MetaboAnalyst

13:25 - MetaboAnalyst History

14:37 - MetaboAnalyst Overview

16:00 - MetaboAnalyst Modules

17:00 - MetaboAnalyst Modules

18:03 - Example Datasets

19:09 - Example Datasets

19:34 - Metabolomic Data Processing

19:44 - Example Datasets

19:45 - Example Datasets

19:45 - MetaboAnalyst Modules

19:48 - Example Datasets

19:48 - Example Datasets

19:49 - Metabolomic Data Processing

19:51 - Common Tasks

20:38 - Select a Module (Statistical Analysis)

20:48 - Common Tasks

20:49 - Metabolomic Data Processing

20:49 - Example Datasets

20:49 - Example Datasets

20:55 - Example Datasets

20:55 - Metabolomic Data Processing

20:56 - Common Tasks

20:56 - Select a Module (Statistical Analysis)

21:07 - Data Upload

21:37 - Alternatively …

22:18 - Data Set Selected

23:24 - Data Integrity Check

24:11 - Data Normalization

25:51 - Data Normalization

26:28 - Data Normalization

27:40 - Normalization Result

29:49 - Data Normalization

29:59 - Normalization Result

30:03 - Data Normalization

30:14 - Normalization Result

30:15 - Data Normalization

30:15 - Data Normalization

30:16 - Data Normalization

30:21 - Data Normalization

30:21 - Data Normalization

30:36 - Normalization Result

31:24 - Data Normalization

31:26 - Next Steps

31:37 - Quality Control

32:41 - Visual Inspection

33:36 - Outlier Removal (Data Editor)

34:01 - Noise Reduction (Data Filtering)

35:09 - Noise Reduction (cont.)

35:36 - Data Reduction and Statistical Analysis

36:07 - Common Tasks

36:30 -

37:00 - ANOVA

37:31 - ANOVA

38:58 - View Individual Compounds

39:46 - What’s Next?

40:06 - Overall Correlation Pattern

41:20 - High Resolution Image

41:53 - What’s Next?

42:40 - Pattern Matching

43:29 - Pattern Matching (cont.)

44:57 -

45:16 - Pattern Matching (cont.)

45:17 - Pattern Matching

45:32 - Pattern Matching (cont.)

45:34 -

45:55 - Multivariate Analysis

46:58 - PCA Scores Plot

47:40 - PCA Loading Plot

47:58 - PCA Scores Plot

48:15 - PCA Loading Plot

49:14 - 3D Score Plot

50:28 -

51:06 - 3D Score Plot

51:07 - PCA Loading Plot

51:08 - PCA Scores Plot

51:46 - PCA Loading Plot

51:47 - 3D Score Plot

51:49 -

52:30 - Multivariate Analysis

52:54 - PLS-DA Score Plot

53:23 - Evaluation of PLS-DA Model

55:19 - Important Compounds

57:07 - Model Validation

58:07 -

58:16 - Hierarchical Clustering (Heat Maps)

58:34 - Heatmap Visualization

58:48 - Heatmap Visualization (cont.)

59:16 - What’s Next?

59:28 - Heatmap Visualization (cont.)

59:29 - Heatmap Visualization

59:32 - Heatmap Visualization (cont.)

01:00:18 - What’s Next?

01:02:45 - Download Results

01:02:56 - Analysis Report

01:03:21 - Select a Module (Enrichment Analysis)

01:03:29 - Metabolite Set Enrichment Analysis (MSEA)

01:04:18 - Enrichment Analysis

01:04:56 - MSEA

01:05:09 - The MSEA Approach

01:05:18 - Data Set Selected

01:06:02 - Start with a Compound List for ORA

01:06:10 - Upload Compound List

01:06:38 - Perform Compound Name Standardization

01:06:55 - Name Standardization (cont.)

01:07:11 - Select a Metabolite Set Library

01:07:46 - Result

01:08:39 - Result (cont.)

01:09:04 - The Matched Metabolite Set

01:09:18 - Phenylalanine and Tyrosine Metabolism in SMPDB

01:09:42 - Single Sample Profiling (SSP)

(Basically used by a physician to analyze a patient)

01:10:14 - Concentration Comparison

01:10:34 - Concentration Comparison (cont.)

01:11:13 - Quantitative Enrichment Analysis (QEA)

01:11:30 - Result

01:11:47 - The Matched Metabolite Set

01:12:02 - Select a Module (Pathway Analysis)

01:12:09 - Pathway Analysis

01:12:57 - Data Set Selected

01:13:03 - Pathway Analysis Module

01:13:09 - Data Upload

01:13:22 - Perform Data Normalization

01:13:38 - Select Pathway Libraries

01:13:54 - Perform Network Topology Analysis

01:14:04 - Pathway Position Matters

01:14:44 - Which Node is More Important?

01:14:54 - Pathway Position Matters

01:14:56 - Which Node is More Important?

01:15:01 - Pathway Visualization

01:17:15 - Pathway Visualization (cont.)

01:17:28 - Pathway Impact

01:17:43 - Result

01:17:54 - Select a Module (Biomarker Analysis)

01:18:58 - Biomarker Analysis

01:19:37 - Select Test Data Set 1

01:19:42 - Data Set Selected

01:20:34 - Perform Data Integrity Check