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DAS for Visual Omics 2009 DAS Workshop Jose Ramon Macias Biocomputing Unit, CNB-CSIC

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Presentation on theme: "DAS for Visual Omics 2009 DAS Workshop Jose Ramon Macias Biocomputing Unit, CNB-CSIC"— Presentation transcript:

1 DAS for Visual Omics 2009 DAS Workshop Jose Ramon Macias Biocomputing Unit, CNB-CSIC jrmacias@cnb.csic.es

2 Visualizing Functional Genomics Visual, as (some) techniques for obtaining primary data are image-based:  In situ hybridization (ISH)  Immunohistochemistry Omics, because......well everything is –omics nowadays ;-)

3  anatomical Gene Expression Mapping ◦ Integrates ◦ Integrates spatial and temporal gene expression data from different sources. ◦ Analyze ◦ Analyze data to find biological relation between genes or structures with similar profiles. ◦ Represents ◦ Represents data in a summarized view.

4  A tool for biologists, not for bioinformaticians ◦ to make easier the access to information related to the anatomical pattern of gene expression in model organisms  An integrative tool ◦ Should include “any” data source of interest

5  DAS has proven as a successful data sharing platform.  Annotations from other genome or proteome sources would be directly integrated.

6  We started addressing two questions: Given a certain anatomical component (retina)......what genes are expressed during development? Acty Cblc Mif Pkia Acty Cblc Pcna Vax1 Pcna Vax1

7  We started addressing two questions: Given a certain anatomical component (retina)......what genes are expressed during development? Given a set of genes......in what anatomical structures they are expressed during development? Calcr Coch Rgs4 …

8 http://biocomp.cnb.csic.es/VisualOmics/aGEM/

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18 EMAP_ReferenceMGI_Reference EMAGEMGI-GXD SymAtlasKEGG BAMS MTB GENSAT OMIM Client (Web browser) DASxVO Annotation servers aGEM Statistics Analysis Annotations

19 PROSENCEPHALON FOREBRAIN MA0000171 EMAP for embryo MA adult MGI GENE IDs Reference System Anatomic term in data base A Anatomic term in data base B Anatomic term reference system ID

20 Theiler Stage 26 Long whiskers TS26, BRAIN EMAP11619

21 http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/entry_points/... EMAP Reference server

22 EMAP Reference server http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/term?query=EMAP800 EMAP800 TS14,future midbrain 14 http://genex.hgu.mrc.ac.uk/Databases/Anatomy/Diagrams/ts14 Homolog to dna, sequence or volmap. Retrieves a reference of the system

23 EMAP Reference server http://biocomp.cnb.csic.es:9090/das/EMAP_Reference/term?query=EMAP800 EMAGE assay 0 ISH EMAGE:116 MGI gene link...

24 Integration of new gene expression data sources: Allen Brain Atlas, Gene Paint. Micro Array data integration. Expansion to other model organisms: rat, zebrafish, Drosophila, and Human.

25 Natalia Jimenez – natalia@cnb.csic.es Joan Segura - jsegura@cnb.csic.es National Institute for Bioinformatics (INB) Juan Jose Vega - jvega@cnb.csic.es CDTI-CENIT :CDTEAM Project Jose Ramon Macias - jrmacias@cnb.csic.es EMBRACE Group Leader Jose Maria Carazo – carazo@cnb.csic.es Biocomputing Unit CNB-CSIC, Madrid

26  Thanks.

27 Alignment Server (Hybrid models) Reference Server (EMDB data) Annotations Server (EMDB metadata) Other DAS systemsDASx3DEM Annotations Servers Structure Reference Server (PDB structures) Genomic Reference Servers Client

28 Alignment Server (Hybrid models) Reference Server (EMDB data) Annotations Server (EMDB metadata) Other DAS systemsDASx3DEM Annotations Servers Client Reference Server (PDB structures) Other genomic Reference Servers

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