Using Genespring Viewer by luckboy


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									Using Genespring Viewer
Access Genespring viewer can be downloaded from To log in you need a username and password, contact for more information.

Main View



Colour Bar

Folders – used to navigate between experiments, gene lists, analysis results, pathways Browser – where data is displayed e.g graphs, pathways, clustering results Colour Bar – colours used in browser, can be changed by either a) right click on browser > display options > colouring tab or b) edit > preferences > colours Opening genome To open the appropriate genome click: file > open genome or array and select the genome to be used: • Arabidopsis Affy 22k – experiments performed using ATH1 array • Arabidopsis Genome – experiments performed using AG array


Viewing experiments and gene lists To view an experiment: • Open “Experiments” folder • Click on experiment on interest to load data • Click on + to open alternative interpretations of the experiment • Click on + to view samples in that interpretation

Selecting gene list To view a gene lists • Click on “Gene lists” folder • Select gene list of interest To change the view click view and select the appropriate view. Right click on browser > display options to change the options of that view e.g. to select samples to view in scatter plot


Working with gene lists Double clicking on a gene lists (or right click > inspect) will display information about the gene list.

Gene list View Notes – Information about how the gene list was generated, including algorithm used, settings used, experiment used. Gene list tab – Details of the genes in the list, including gene name, AGI code and other annotations. • • • • • • Configure columns – select annotation fields to view Save to file – save gene lists and annotations as .txt file Copy to clipboard – copy gene list information to the clipboard and paste into excel / word etc GO Ontology Browser – view the gene list based on their GO ontologies Copy from workgroup server – copy gene list to local copy Export as zip – export gene list as genespring zip file which can be loaded into Genespring GX

Double clicking on an individual gene will display the expression levels of that gene in the selected experiment and links to external data bases Similar list tab – displays the correlation and overlap with other gene lists -3-

Downloading gene list information • Select gene list of interest • Click edit > copy > copy annotated gene list • Select data and annotations required • Either copy to clipboard or save as .txt file

Copy annotated gene list GO Ontology browser Displays gene lists based on their GO ontology’s. Click on “GO ontology browser” in gene list details. Browser can display the ontology’s in two forms: 1. Pie chart • Select GO ontology category from list on left – biological process, cellular component, molecular function • Double clicking on segment takes you down a level in the annotations • Right click on a segment to save as a gene list 2. Table • Select GO ontology category from list on left – biological process, cellular component, molecular function • Select p-value cut-off in “maximum p-value” box • List can be ordered by clicking any column header • Table can be copied to clipboard or saved as .txt file • Click on category and click on “make list” to save a gene list


GO Ontology Pie Chart

GO Ontology browser table view


Venn diagram of gene lists Venn diagrams can be generated using 2 or 3 gene lists to show the overlap of those lists. These can be made in two ways: • Choose colour bar > colour by Venn diagram • Drag and drop gene lists into segments • Click “show all genes” to set this list as universal list Alternatively • Right click on first gene list > Venn diagram > left • Right click on second gene list > Venn diagram > right • Right click on third gene list > Venn diagram > bottom Creating gene lists from overlaps • Right click on overlap segment of interest • Choose “make gene list” • Save list on local machine or workgroup by choosing folder

Venn Diagram view


Analysing genes of interest There are two main ways of analysing genes of interest in data sets. Single genes • Click edit > advanced find genes • Search by AGI code, Affymetrix probe set ID, keyword • Select the gene of interest by clicking on it • Choose “Select” to highlight the gene in the main view • Choose “Inspect” to view detailed gene information including signal values and links to external databases • Choose “Make gene list” to make a gene list of selected genes

Advanced Gene search

Multiple genes • Create a gene list in word, notepad, excel, of AGI codes or Affymetrix probe set ID’s • Copy list to clipboard • In Genespring viewer click edit > paste > paste > paste gene list • Choose a name and save – Gene lists can be saved on your local machine or on the workgroup, by selecting appropriate folder


Folders on Genespring Workgroup Folders on local machine

Saving Gene list

Downloading .CEL files There are a number of ways of downloading .CEL files from the Workgroup: 1. Using Sample Manager • Choose Experiments > Sample manager • Can view all samples or filter on experiment, parameter, attribute, keyword • Select sample of interest • Choose “Inspect” • Choose “Associated files” tab and select .CEL file • Choose “Extract file” and save file • Choose .txt file to download RMA normalised data 2. Using sample inspect • In main window select experiment of interest • Open “all samples” interpretation • Right click on sample of interest > inspect • Choose “Associated files” tab and select .CEL file • Choose “Extract file” and save file • Choose .txt file to download RMA normalised data


Sample Manager

Sample Inspector


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