系统生物学软件（王栋）Expander5 workshop_April11-handouts.docVIP

Expander v5.2.2 – hands-on session: Launching Expander: In your Expander (5.2._) directory double click on Expander.bat. Before starting please create a directory named “results” in the Expander5.2.2 directory. Human stem cells analysis: In this section, we will analyze a dataset published by Mueller et al. (Nature 2008) in which high-density Illumina oligonucleotide array data was used to measure expression profiles from different cell lines, including embryonic stem cells (ESCs), neural stem cells (NSCs), differetiated cells and two placenta cancers. Loading the data: From the “File” menu, select “New Session” ( ”Expression Data” ( “Tabular Data File”. In the “Load Study” dialog box, make sure the Organism is set to “Human”. Use the “Browse” button and search for the file stemCells.raw.txt. Select the option “Use probe Ids as gene Ids”. Make sure that the “Data type” is set to “Absolute Intensities”. Press the “Advanced” button. In the “Advanced” Dialog box select “Autofill symbols” and press “OK”. Press “OK” in the ”Load Study” dialog box. If a question pops up asking if you would like to download data for human, press Ok and wait for the download process to end. Preprocessing the data: From the “Preprocessing” menu, select “Normalization” ( “Quantile”. From the “Preprocessing” menu, select “Log Data”. Using t-test statistics to detect differential expression: From the “Supervised Grouping” menu, select “Differential Expression” ( “t-Test”. In the “Requested type of change” combo-box select “Differential”. Press the “Select” button for the “Group 1 conditions”. In the “Select Conditions” dialog box, check (mark) all groups (check boxes) except for the last one (“Cancer”) and press “OK”. Press the “Select” button for the “Group 2 conditions”. In the “Select Conditions” dialog box, check (mark) the “Cancer” check box’ and press “OK”. Press “Ok”. Look at the resulting groups on the left. Click on the pattern chart of the down-regulated group. A table w