Tutorial
Retrieving Genomic information for a specific gene

- Using Molecule Search and GBrowse.

This video shows how to query COMPARE for a specific gene

Here: "Zebrafish FGF8 gene".

- A synoptic gene report displays the annotations and several features collected and organized for this gene.
- Genomic information are available through the "GBrowse" tool. GBrowse is available by clicking on the image representing the gene whithin its chromosome context.
- In GBrowse one can visualize the location of the gene of interest within the chromosome and information about neighboring genes.
- The exon/intron structure is available by clicking on the spliced transcript.

Searching for genes expressed in specific anatomical parts at a given developmental stage with the "in situ search tool"

- Using in situ search.

This video shows how to search for genes expressed in specific anatomical parts at a given developmental stage with the "in situ search tool"

Here: Zebrafish genes expressed in myotome and heart at Pharyngula: Prim 25 stage.

- This search is possible through "insitu search" tool.
- When a species is selected, all available developmental stages are displayed.
- Choose one of them, here: Pharyngula: Prim 25 stage.
- The search can be launched for all genes expressed at this stage.
- However in the demo, we refine our search for genes expressed in specific anatomical parts (myotome and heart), using the "Add term button".
- An anatomical term selector appears. Users can add specific terms using the auto complementation text area or by browsing through the anatomical tree.

Searching for genes involved in several pathways using the "Pathway search tool"

- Using Pathway search and Boolean connectors.

This video shows how to retrieve genes involved in several pathways

Here: Human genes involved in "MAPK signaling pathway" AND in "Regulation of actin cytoskeleton ".

- This search is possible with the "Pathway search" tool.
- When a species is selected, all available pathways are displayed.
- Choose several pathways with the Crtl - key.
- Apply a Boolean connector (possibilies: AND/OR and AT LEAST/ONLY).
- Here we choose AND and AT LEAST.
- All genes that are involved (at least) in both pathways are shown.
- Verification: choose one gene. In its report, the two pathways that we started with are found.


Transfer of information using the orthology prediction tools

- Using molecule search,orthology predictions, expression data.

This video shows how to retrieve expression information for a gene which has no associated expression data, using the orthology prediction tools found in COMPARE.

Here: The Drosophila gene CG10250.

- CG10250 has no associated in situ hybridization data.
- Predicted orthologs are found in Zebrafish, mouse and human.
- Note that orthologs can be predicted by one, two or three methods.
- In situ hybridization data are available for Zebrafish and for mouse.


Refine a set of genes

This video shows how to refine a set of genes.

Here: Zebrafish "membranal" genes that are expressed in somite at Segmentation:14-19 somites Stage.

- Using in situ search, retrieve genes that are expressed in "somite" at 14-19 somites stage .
- Using this set of genes as an entry point for gene ontology search.
- Search for genes with GO annotations : "membrane" and "integral to membrane".


Compare set of genes between species

- Using in situ search, refine tool, Batch query tool and Orthologs transfer.

This video shows how to retrieve additional information from a set of genes and their orthologs predicted by X methods.

Here: Which are the GO and the Pathways annotations for Zebrafish genes expressed in "Myotome" at Pharyngula:Prim-5 Stage.

- Using in situ search, retrieve genes that are expressed in "Myotome" at Pharyngula:Prim-5 Stage .
- Using this set of genes as an entry point for the Batch query tool.
- Search for GO and Pathways annotations known for these genes.
- Export these data into Spreadsheat software.
- Get the GO and Pathways for their orthologs predicted by 4 orthology prediction methods.