GV Exercise.7

Create a probe signature and search for similar conditions

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| GV Exercise.8 ]
last edit: October 31, 2014

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Aim

Create new signature in GV or use published signatures to find other conditions where expression profile of the signature set is similar.

signatures can group UR and DR markers to better describe biological networks

Find ABA-1h top [UR & DR] probes in one experiment (AT-00110; 48 samples)

• create a new Sample Selection for the experiment AT-00110 (hormone stimulations)

try it first

• use gene Search perturbation to find top 10 probes with log-ratio of >+2 AND max 10 probes with log-ratio of <-2 after 1h treatment with ABA

ABA markers

• export results to excel files and open the 2 files in a worksheet editor

AT-00110-10UR.xls

AT-00110-5DR.xls

• merge probe IDs and log-ratio values for ABA-1h UR and DR probes to a new sheet and transpose (col<->rows)

try it first

Create a probe signature for ABA

The signature tool finds conditions where a table of UR and/or DR markers provided by the user are found with similar differential expression. Such table can be generated in GV or built manually if you have a list of genes in mind that describes your biological model. When users do not have expression data, arbitrary values can be attributed to each gene to indicate the direction of DE (>0 for UR, and <0 for DR expressed in log scale).

• copy the two column block for UR and DR probes and paste it in the signature tool

try it first

Run the signature tool to find other similar conditions within AT-00110

We use as signature, the table produced earlier.

• keep Sample Selection to AT-00110

try it first

• setup the signature tool

try it first

• review most similar perturbations

try it first

• review most different perturbations

try it first

Run the signature tool to find other similar conditions within all A.th perturbations in GV

To do so, change Sample Selection to Ath.all set and repeat both queries

• review most similar perturbations

try it first

• review most different perturbations

try it first

You can again save any of these tables with values and use them for functional enrichment as shown in GV_Exercise.4#Perform_GSEA_with_the_Plant_GSEA_web-portal

Download the exercise files

Try it by yourself before expanding on the right!

• download ex7.gv4 and open it from within genevestigator File Load Workspace link
• download the AT-00110 signature worksheet link

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References:

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[ Main_Page | Genevestigator_training | Analyze_public_microarray_data_using_Genevestigator | GV Exercise.6 |
| GV Exercise.8 ]