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Overview of Genevestigator

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Presentation on theme: "Overview of Genevestigator"— Presentation transcript:

1 Overview of Genevestigator

2 Content Introduction Tools Additional tips Metaprofile analysis
Biomarker search RefGenes Clustering analysis Additional tips

3 Concept of Genevestigator
Tissue type 1 Tissue type 2 Tissue type 3 Tissue type 4 Tissue type 200 Thousands of microarray experiments world-wide Curation of data and annotation Model of a summarized output Curation: normalization and annotation of - Anatomy - Development - Stimulus and Mutation Establishment of the Genevestigator Database

4 Curation: quality control of microarray data
Unprocessed probe intensity RNA degradation plots Probe-level analysis (RLE, NUSE) Border element analysis Array-array correlation plots

5 Overview of the Genevestigator System
Database and Application Server Cluster Website Java Client Application


7 Genevestigator CLASSIC tool: Meta Profile Analysis

8 Meta Profile Analysis: analytical approach
genes Anatomy [space] Development [time] Stimulus / Mutation [response] which conditions?

9 Meta-Profile Analysis
1. Chose an organism 2. Enter the genes you wish to work with

10 Meta-Profile Analysis
View and interpret the results across: Anatomical categories (Anatomy tab) Developmental stages (Development tab) Chemicals, diseases, treatments, etc. (Stimulus tab) Genetic modifications (Mutation tab) Tumor types (Neoplasm tab)

11 Meta-Profile Analysis: Anatomy tool
Looks at how genes are expressed in different tissues Mean and standard deviation Anatomy categories as a tree (ontology); expand / collapse Number of arrays per category is indicated Looks at how genes are expressed in different tissues Mean and standard deviation Anatomy categories as a tree (ontology); expland / collapse Number of arrays per category is indicated Anatomical expression profile of ß-Actin in the mouse

12 Meta-Profile Analysis: Development tool
Looks at how genes are expressed during the life cycle of an organism Example for human Example for mouse / rat Expression profile of BDNF across the human development

13 Meta-Profile Analysis: Stimulus and Mutation tools
Most upregulating conditions List (or tree) of various conditions Spots indicate the responses of selected gene(s) to the list of conditions Most downregulating conditions

14 Meta-Profile Analysis: Neoplasm tool
Looks at how genes are expressed in different tumors Mean and standard error Tumors ordered as a tree (ontology); expand / collapse Number of arrays per category is indicated Looks at how genes are expressed in different tissues Mean and standard deviation Anatomy categories as a tree (ontology); expand / collapse Number of arrays per category is indicated Expression profile of NPY1 receptor across human tumors

15 Genevestigator ADVANCED Tools

16 Biomarker search: analytical approach
conditions which genes? Anatomy [space] Development [time] Stimulus / Mutation [response]

17 Biomarker search 1. Chose an organism
2. Chose conditions and run analysis 3. Save target genes for further analysis

18 Biomarker Search Identify genes that exhibit specific expression characteristics Anatomy Development Stimulus / Mutation

19 Biomarker Search in Genevestigator
target condition condition 1 condition 2 condition 3 condition 4 condition 5 condition 6 condition 7 condition 8 condition 9 condition 10 condition 11 condition 12 condition 13 condition 14 condition 15 condition 16 condition 17 condition 18 condition 19 condition 20 condition 21 condition 22 condition 23 condition 24 condition 25 condition 26 condition 27 condition 28 condition 29 condition 30 condition 31 condition 32 condition 33 condition 34 condition 35 condition 36 condition 37 condition 38 condition 39 condition 40 condition 41 condition 42 condition 43 condition 44 condition 45 condition 46 condition 47 condition 48 condition 49 condition 50 condition 51 condition 52 condition 53 condition 54 condition 55 condition 56 condition 57 condition 58 condition 59 condition 60 condition 61 condition 62 condition 63 condition 64 condition 65 condition 66 condition 67 condition 68 condition 69 condition 70 condition 71 condition 72 condition 73 condition 74 condition 75 gene 3 gene 5 gene 7 gene 13 gene 17 gene 10 gene 2 gene 15 gene 9 gene 12 gene 4 gene 11 gene 16 gene 1 Imagine extending this to a much wider set of conditions… you may find other conditions to which the set of genes respond gene 6 gene 8 gene 14 other conditions to which the genes are responding

20 Biomarker Search in Genevestigator
Example: human genes responsive to Actinomycin-D target condition(s) Actinomycin-D vMyb Oncolytic herpes simplex virus Propiconazole Sapphyrin Echinomycin Cell cycle inhibition co-inducing conditions Chemical: ARC

21 RefGenes – find the best housekeeping genes
Validation experiment on mouse liver geNorm selection of the most stable reference genes within this experiment Dataset: 197 arrays from mouse liver

22 Clustering Analysis Goal: to identify groups of genes that have similar expression characteristics Tools: Hierarchical clustering (with leaf ordering) Biclustering (BiMax algorithm)

23 Hierarchical clustering
Cluster sets of genes expressed at different stages of plant development HC using leaf ordering algorithm

24 Biclustering Search for biclusters in a list of 64 genes responsive to myocardial infarction One of many possible biclusters Development profile of these 7 genes

25 GENEVESTIGATOR Useful features

26 Useful features - tooltips
Tooltips (mouse-over) provide detailed information about a treatment, a spot, or an experiment.

27 Focus function Focus on an array selection Focus on a gene selection
tools will compile results from this combination of data allows to easily jump from one selection of genes or arrays to another selection Note: be sure that genes and organism/arrays are compatible! (e.g. you cannot look at mouse genes in a selection of rat arrays…) 27

28 Exporting figures scale export image Save export image in: PNG JPEG

29 Exporting data Export content: Mean value Standard error values
Export format: tab-delimited (TXT) or comma-separated (CSV)

30 Saving workspaces Saves content of selections:
selections of experiments and arrays selections of genes status of checkboxes Benefits: allows to share results between colleagues allows to continue your research at a later stage without losing the context

31 GENEVESTIGATOR End of presentation

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