Ontology based analyses methods
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Ontology based analyses methods ++. develop a grammar for making productions using mf, bp, cl: derive a higher level grammar for next level of productions  derive a formal annotation language? Add structure awareness : Create an iconic mapping for cl terms to facilitate novel analyses.

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Ontology based analyses methods ++

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Ontology based analyses methods

Ontology based analyses methods ++

  • develop a grammar for making productions using mf, bp, cl:

    • derive a higher level grammar for next level of productions  derive a formal annotation language?

  • Add structure awareness: Create an iconic mapping for cl terms to facilitate novel analyses.

  • Add time awareness: express the temporal dimension and have time-dependent annotations


Go based analysis of microarray data

GO based analysis of microarray data


Tf binding site annotation data

TF-binding site & Annotation data

TF-sites show that the ABRE and GBF sites are enriched in these genes.

Component and function annotations show that these genes are located in the chloroplast thylakoid membrane, are part of the light-harvesting complex and have the molecular function of chlorophyll binding and electron transport.


Clench is useful but we need more

Clench is useful … but we need more!

  • Clenchhelps the biologist interpret a list of genesand form a result statement such as:

    • The photosynthesis genes located in the chloroplast are repressed in response to ozone stress and have the ABRE binding site enriched in their promoters.

  • More at www.personal.psu.edu/nhs109/Clench


Within ontology grammars

Within-ontology “grammars”

OBOL

Relations Ontology


Between ontology grammars

Between-ontology “grammars”

?<link>?

<Some MF> in <Some BP>


Payoff if we have between ontology grammars

Payoff: If we have between-ontology grammars

  • We can systematically store the interpretations (or results) of GO based analyses

  • We can browse [gene-expression] data in [particular ontology] centric views

    • Work of Gennari et al

  • We can create semantically rich annotations that span multiple ontologies.


Storing go based analysis reports

Storing GO based analysis reports

The photosynthesis genes located in the chloroplast are repressed in response to ozone stress and have the ABRE binding site enriched in their promoters.

The genes of the photosynthesis proteins located in the chloroplast show a decrease in their mRNA level in response to ozone stress and have the ABRE binding site enriched in their promoters.


Anatomy centric views by gennari et al

Established links between the cellular structure terms in FMA and the GO cellular component terms

Did it for 150 terms

Established links between tissue-region annotations and brain anatomy terms in FMA

Anatomy centric views by Gennari et al

Cyclin D1 is associated with cellular proliferation in colon

Cyclin D1 is associated with neuronal degeneration in brain

Cyclin D1 has <mf> in cellular proliferation in colon


Semantically rich annotations

Semantically rich annotations

HOW

WHY


Ontology based analyses methods1

Ontology based analyses methods ++

  • develop a grammar for making productions using mf, bp, cl:

    • derive a higher level grammar for next level of productions  derive a formal Annotation language?

  • Add structure awareness: Create an iconic mapping for cl terms to facilitate novel analyses.

  • Add time awareness: express the temporal dimension and have time-dependent annotations


What about 3d structure of the cell

What about 3D structure of the cell?


Payoff if we have iconic mappings

Payoff: If we have iconic mappings

  • We can browse ontologies in an anatomy centered manner

  • Can use these new views for facilitating the annotation process

    • i.e. improve curator  annotation tool interaction

  • Create novel visualizations forinterpreting high dimensional datasets.

    • Time course data [coming few slides later]

    • Integrating gene expression, protein expression and metabolomic datasets.


Ontology based analyses methods2

Ontology based analyses methods ++

  • develop a grammar for making productions using mf, bp, cl:

    • derive a higher level grammar for next level of productions  derive a formal Annotation language?

  • Add structure awareness: Create an iconic mapping for cl terms to facilitate novel analyses.

  • Add time awareness: express the temporal dimension and have time-dependent annotations


What about the temporal dimension

What about the temporal dimension?

Overlay time course data onto the GO tree.

See how the ‘enriched’ categories change over time.

Understand the dynamics of the biological phenomenon being studied.

  • Will complement pathway based analysis approaches


How about cell structure and time

How about cell structure and time?


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