course on functional analysis - cniobioinfo.cnio.es/files/training/functional_analysis... ·...
TRANSCRIPT
![Page 1: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/1.jpg)
Gonzalo Gómez, PhD. [email protected]
Madrid, June 12nd, 2007.
::: information Hiperlinked Over Proteins - iHOP -
Course on Functional Analysis
Bioinformatics Unit CNIO
![Page 2: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/2.jpg)
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 genes H. sapiens, M. musculus, D. melanogaster…more than 1500 organisms
![Page 3: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/3.jpg)
information hiperlinked Over proteins - iHOP -
::: Main Window.
http://www.ihop-net.org/
![Page 4: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/4.jpg)
information hiperlinked Over proteins - iHOP -
::: Help.
![Page 5: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/5.jpg)
information hiperlinked Over proteins - iHOP -
::: Searching genes.
Results options
![Page 6: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/6.jpg)
::: Results options.
Defining Information for this Gene
Open Abstract High Impact Journal
Open Abstract
Add this Sentence to Gene Model Main gene
Associated genes Relevant Biomedical terms Compounds
Colour legend
![Page 7: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/7.jpg)
::: 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).
![Page 8: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/8.jpg)
information hiperlinked Over proteins - iHOP -
::: Results options.
Most Recent Information for this Gene
Minimal Information for this Gene
No literature info
![Page 9: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/9.jpg)
information hiperlinked Over proteins - iHOP -
::: Gene model.
Gene model is a interactive graph where you can add interesting sentences and interactions.
![Page 10: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/10.jpg)
information hiperlinked Over proteins - iHOP -
::: iHOP Confidence Value.
The synomnym ambiguity limitation Many 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 value Although no definite solution for the problem of synonym ambiguity is in sight, it is possible to put an automatically derived 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.
![Page 11: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/11.jpg)
::: End Points . . .
![Page 12: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/12.jpg)
http://gepasmirror.bioinfo.cnio.es/gepas/
::: GEPAS mirror at CNIO.
![Page 13: Course on Functional Analysis - CNIObioinfo.cnio.es/files/training/Functional_Analysis... · Gonzalo Gómez, PhD. ggomez@cnio.es Madrid, June 12nd, 2007.::: information Hiperlinked](https://reader033.vdocuments.net/reader033/viewer/2022060303/5f08df6b7e708231d4242266/html5/thumbnails/13.jpg)
::: AKS2
Next course Edition :::