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1 GENEVESTIGATOR Overview of Genevestigator. Content Introduction Tools Metaprofile analysis Biomarker search RefGenes Clustering analysis Additional.

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Presentation on theme: "1 GENEVESTIGATOR Overview of Genevestigator. Content Introduction Tools Metaprofile analysis Biomarker search RefGenes Clustering analysis Additional."— Presentation transcript:

1 1 GENEVESTIGATOR Overview of Genevestigator

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

3 Concept of Genevestigator 3 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 4

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

6 6 GENEVESTIGATOR Tools

7 7 Genevestigator CLASSIC tool: Meta Profile Analysis

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

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

10 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 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 Anatomical expression profile of ß-Actin in the mouse

12 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 13 Meta-Profile Analysis: Stimulus and Mutation tools List (or tree) of various conditions Most upregulating conditions Most downregulating conditions

14 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 Expression profile of NPY1 receptor across human tumors

15 15 Genevestigator ADVANCED Tools

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

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

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

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

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

21 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 22 Clustering Analysis Goal: to identify groups of genes that have similar expression characteristics Tools: –Hierarchical clustering (with leaf ordering) –Biclustering (BiMax algorithm)

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

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

25 25 GENEVESTIGATOR Useful features

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

27 27 Focus function Note: be sure that genes and organism/arrays are compatible! (e.g. you cannot look at mouse genes in a selection of rat arrays…) 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 27

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

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

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 30

31 31 GENEVESTIGATOR End of presentation


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