Pathway analysis. Martina Kutmon Department of Bioinformatics Maastricht University

Transcription

1 Pathway analysis Martina Kutmon Department of Bioinformatics Maastricht University

2 Who are we? Department of Maastricht University Martina Kutmon PhD student, 3rd year Anwesha Bohler PhD student, 2nd year Egon Willighagen PostDoc

3 What's gonna happen today? Pathway Analysis Introduction Quiz Hands-on session Introduction to the dixa project data warehouse ArrayAnalysis.org quality control, normalization, statistical analysis of microarray data

4 What's gonna happen tomorrow? Network Analysis Introduction Quiz Hands-on session ConsensusPathDB interaction database

5 Outline 1. What are biological pathways? 2. Where can we find pathway data? 3. How can we create pathways? 4. Why pathway analysis? 5. Introduction of the Quiz and Hands on session

6 Outline

7 1. What are biological pathways?

8 1. What are biological pathways?

9 1. What are biological pathways?

10 1. What are biological pathways?

11 1. What are biological pathways?

12 1. What are biological pathways?

13 What are biological pathways? Definition in Wikipedia: "... a series of actions among molecules in a cell that leads to a certain product or a change in a cell." Types: Metabolic pathways Gene regulation pathways Signal transduction pathways

14 What are biological pathways?

15 Metabolic pathways "... series of chemical reactions occurring within a cell." Enzymes catalyze these reactions. Example: Glycolysis

16 Metabolic pathways

17 Gene regulation pathways Pathways that regulate the level of gene expression Often sub-pathway in a larger pathway Linked to gene regulatory networks

18 Signal transduction pathways Signaling pathways Cellular responses to extracellular stimulation Initial stimulus can trigger several steps resulting in physiological events like the increased uptake of glucose from the blood stream

19 Signal transduction pathways MAPK pathway

20 Signal transduction pathways MAPK pathway

21 2. Where can we find pathway data?

22 Pathway Resources pathway data interaction data WikiPathways, KEGG, Reactome, Panther, BioCarta, ConsensusPathDB, BioCyc, PathwayCommons,...

23 Pathway Resources BUT... still a lot of information missing in online pathway resources Only ~30% of the known human genes are present in a pathway Existing knowledge carefully hidden in Literature Researchers

24 Biological Knowledge

25 Biological Knowledge

26 Biological Knowledge

27 WikiPathways A wikipedia for pathways... everybody can contribute and share pathways everybody can edit and curate pathways everybody can use the pathway collection not just diagrams but fully annotated pathways interactive pathway viewer integrated pathway editor changes can be reverted easily new findings can be added immediately

28 WikiPathways Statistics: 1769 pathways 557 curators (>8500 registered users) >200 edits per month

29 Pathway Curation Community efforts Portals: Plants - Gramene database WormBase - C.elegans pathways CIRM - stem cell related pathways Reactome - manually curated database... Question of data quality? curation tags to indicate the status/ quality of the pathway

30 Pathway Curation Curation Tags

31 Search and Browse Pathways

32 Search and Browse Pathways

33 Pathway Curation

34 Annotations Add annotations (external references, publication references, comments) to: Data nodes (Gene Product, Metabolite, Protein, Rna, Pathway, Unkown) Whole pathway diagram Interactions

35 Identifier mapping with BridgeDb is an identifier mapping framework for bioinformatics applications provides gene product mapping databases for several species provides metabolite mapping database provides interaction mapping database (in testing) For more information, see

36 Identifier annotations Annotations of data nodes and interactions with Xrefs (= identifier + data source) DataSource Ensembl NCBI Gene HMDB Rhea Identifier ENSG HMDB01401 RHEA:13068 Pathway 1 Pathway 2 Ensembl NCBI Gene ENSG BridgeDB knows that those represent the same biological entity

37 Identifier mapping WikiPathways BridgeDb is integrated in the infrastructure, so the identifiers are mapped automatically PathVisio Load BridgeDb identifier mapping databases for GeneProducts and Metabolites Use BridgeDb to solve your own mapping problems

38 Pathways in Bioinformatics tools GenMAPP PathVisio Cytoscape GO-Elite Webservice API Export to BioPAX - semantic web SPARQL endpoint

39 3. How can we create pathways?

40 Pathway Creation summary/review and organisation of existing knowledge machine-readable representation of a hypothesis

41 Pathway Creation Advantages of a pathway in GPML format: Machine-readable Fully annotated (identifiers, references) Graphical elements for better understanding Share pathway on WikiPathways Perform pathway analysis with PathVisio Use BridgeDb to solve identifier mapping issues Further analysis: Open the pathway as a network in Cytoscape

42 Tips and Tricks Create your pathway offline in PathVisio and upload it in one step to WikiPathways Annotate your data nodes from the beginning! Then you can visualize your data immediately on the pathway. Add all your reference articles. You will remember where you found what information and your pathway diagram can be your bibliography.

43 Tips and Tricks Visualize multiple data sets simultaneously, time series data or multi-omics data on pathways. Visualize data on the interactions in the pathway diagram - flux data, confidence scores,... Export your pathway diagrams with or without data to share, publish and present your work.

44 Tips and Tricks WikiPathways allows multiple versions of the same pathway in different settings (organisms, disease state, cell type). PathVisio allows you to change font, font size, color, line thickness, line color,... Add graphical elements to make your pathway diagram unique.

45 Tips and Tricks WikiPathways allows multiple versions of the same pathway in different settings (organisms, disease state, cell type). PathVisio allows you to change font, font size, color, line thickness, line color,... Add graphical elements to make your pathway diagram unique.

46 Short live demo of WikiPathways

47 4. Why pathway analysis?

48 Why Pathway Analysis? Microarray analysis workflow

49 Why Pathway Analysis?

50 Why Pathway Analysis? "A image says more than a thousand words." Intuitive Puts data in biological context More efficient and useful than looking up single gene information Computational analysis Overrepresentation analysis Network analysis

51 Z-Score statistics Find "enriched" pathways: Statistical method: Z-Score analysis Other enrichment calculation methods: Ackermann M et al., A general modular framework for gene set enrichment analysis, BMC bioinformatics, 2009

52 Z-Score statistics Find "enriched" pathways: Statistical method: Z-Score analysis Other enrichment calculation methods: Ackermann M et al., A general modular framework for gene set enrichment analysis, BMC bioinformatics, 2009

53 Z-Score statistics Ranking method: High Z-Score --> selection is very different from the rest of the dataset Z-Score > 1.96 = significant

54 PathVisio Presenting and exploring biological pathways within PathVisio. Van Iersel et al. PubMed:

55 PathVisio 3 PathVisio 3 released since end of March New modular system Extension with plugins Plugin manager allows installation of plugins in the repository Building up repository with existing plugins (9 plugins present, ~10 more in submission process)

56 PathVisio application

57 PathVisio repository Plugin repository - org/plugins/plugins-repo/

58 PathVisio plugin manager

59 PathVisio Analysis Workflow Data preparation Import data in PathVisio Visualize data on pathways Export pathway images Find enriched pathways

60 Data preparation PathVisio accepts delimited text files Prepare and export from Excel

61 Data import Identifier mapping!

62 Identifier and System Code A system code is a 1 or 2 letter code for a biological database: - En for Ensembl - L for Entrez Gene - X for Affymetrix

63 ID Mapping Databases BridgeDb mapping databases (.bridge) files For gene products and metabolites Database for interactions under testing Your data A pathway L L L L L L L L: 153 En: ENSG S: Q53GA5

64 Identifier and System Code identifiers system code

65 Exception File Exceptions will show up here

66 Pgex File Imported data is stored in a.pgex file

67 Data Visualization

68 Data Visualization Color set based on gradient (log FC)

69 Data Visualization Color set based on criterion / rule (p value)

70 Data Visualization

71 Statistical Analysis Define a criterion and a pathway collection

72 Statistical Analysis Results = list of pathways

73 Export as Image High quality images for publications or presentations

74 Acknowledgements

75 Questions?

76 5. Introduction Quiz and Hands-on Session

77 Quiz Work alone or in groups Get familiar with the tools

78 Hands on session Data: from dixa data warehouse (you need username and password to access the dataset!) repeated dose 14-day toxicity study in adult male rats chemical compound - FP003SE pathway analysis with liver data --> high-dose vs. control

79 Hands on session After quiz and coffee Instructions available on projects.bigcat.unimaas.nl/ebi-roadshow/