Daniel Rico, PhD. drico@cnio.esDaniel Rico, PhD. drico@cnio.es

Madrid, February 16th, 2010.Madrid, February 16th, 2010.

::: information Hiperlinked Over Proteins - iHOP - ::: information Hiperlinked Over Proteins - iHOP -

Course on Functional AnalysisCourse on Functional Analysis

Bioinformatics UnitCNIO

Bioinformatics UnitCNIO

information hiperlinked Over proteins - iHOP -

::: Introduction.

A Gene Network for Navigating the Literature.

Hoffmann, R., Valencia, A. Nature Genetics 36, 664 (2004)

User-Friendly Text mining tool Searches into PubMed abstracts

Uses genes and proteins as hyperlinks between sentences and abstracts. iHOP converts PubMed information into one navigable resource.

80.000 different genesH. sapiens, M. musculus, D. melanogaster…more than 1500 organisms

information hiperlinked Over proteins - iHOP -

::: Main Window.

http://www.ihop-net.org/http://www.ihop-net.org/

information hiperlinked Over proteins - iHOP -

::: Help.

information hiperlinked Over proteins - iHOP -

::: Searching genes.

Results options

::: Results options.

Defining Information for this Gene

Open AbstractHigh Impact Journal

Open Abstract

Add this Sentence to Gene ModelMain gene

Associated genesRelevant Biomedical termsCompounds

Colourlegend

::: Results options.

Interaction Information for this Gene

Interaction experimental

evidence

Use the Filter and options menu to include or exclude specific experimental data sets.

etc.

This view contains all sentences found in the literature for the main gene of a page (gene A) and other genes (gene B).

information hiperlinked Over proteins - iHOP -

::: Results options.

Most Recent Information for this Gene

Minimal Information for this Gene

No literature info

information hiperlinked Over proteins - iHOP -

::: Gene model.

Gene model is a interactive graph where you can add interesting sentences and interactions.

information hiperlinked Over proteins - iHOP -

::: iHOP Confidence Value.

The synomnym ambiguity limitationMany gene or protein synonyms are ambiguous, thus one and the same synonym is often used for different genes. Even human experts can have difficulties to resolve such ambiguities and automatic systems, like iHOP, will therefore always exhibit certain errors.

The iHOP confidence valueAlthough no definite solution for the problem of synonym ambiguity is in sight, it is possible to put an automaticallyderived confidence value to specific gene references. This iHOP confidence value is illustrated through the colour intensity of a star

The absence of a star does not mean that a certain term could not be a gene, but simply that supporting evidence is not available.

::: End Points . . .

http://gepasmirror.bioinfo.cnio.es/gepas/http://gepasmirror.bioinfo.cnio.es/gepas/

::: GEPAS mirror at CNIO.

::: AKS2

Next course Edition :::

Thanks !!ggomez@cnio.es