- This tutorial has two parts, click and move easily.

Go to tutorial for Expression Profiling
Go to tutorial for DEG Analysis





Tutorial 1. Expression Profiling


This is a procedure for browsing one of the probes with anotation of "fibroblast growth factor 4" in gene description from GPL570 platform as a demo running. There are three major steps in this module.




Step 1 : Search Probe Index

1) Click "Search Probe Index" button on the main page. You will have new browser with following dialog      contents.



2) Type "fibroblast growth factor 4" in the "Keyword" field.

3) Select "Gene Description" from "Search field" pull down menu.

4) Select "GPL570, Affymetrix GeneChip Human Genome U133 Plus 2.0 Array" from "Platfrom(GPL)" field.

5) Click "Search" button, then you will have the info. of retrieved probe IDs as follows.





6) Click one of "select" buttons, which corresponds to probe ID of interest. It will place the selected probe ID on      the "probe ID"field on the GS-Profiling module in the main page. Then, go back to main GS-LAGE page.





Step 2 : Expression Profiling



1) Select "GPL570" from "GPL ID" pull down menu.

2) Click "Search", then you will have "LAGE PROFILE" window for browsing GS-LAGE score values.





Step 3 : Browsing GS-LAGE score values on "LAGE PROFILE" window.



In this window, we can browse the GS-LAGE scores within same GPL platform. Note that x-axis represents the index number for Array Samples and y-axis GS-LAGE score values.

1) Place the mouse cursor on any region of the "Lage Profile" on the chart. You can retrieve the GS-LAGE      score of selected sample as above.

2) Click the selected sample and you will have the new browser as below. This window contains the information      of selected GDS data set and all GSM samples of selected GDS.





3) "Zooming" function.



You can find the control bar for zooming in or out the "Global Expression Profile" on the bottom right of "LAGE PROFILE" window. For zooming in, move the slider control to the right or click the "<>" button. For zomming out, move the slider control to the left or click the "><" button.



4) "Display option" function.



You can find the pull-down menu for "Displaying Option". There are three options displaying global expression profiles for 1)Raw expression, 2)LAGE score, 3)both Raw expression and LAGE score.




5) "Filtering" function.



You can find the pull-down menu for filtering samples on the top of "LAGE PROFILE" window. For selecting samples greater than certain GS-LAGE score, select "V greater than" option from the menu and put the cutoff value of GS-LAGE score, and click "Go" button. Then, you will have the refreshed "LAGE PROFILE" window with filtered GS-LAGE scores as below. You can filter the GS-LAGE score less than the cutoff value by choosing "V less than" option from the menu. For filtering raw expression values, choose "U greater than" or "U less than" option from the menu in similar way.








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Tutorial 2. DEG Analysis




This is a procedure for analysis of differentially expressed genes(DEG Analysis) with "breast cancer"-related GEO data sets from GPL570 platform as a demo running. There are three major steps in this module.





Step 1 : Search GEO Index

1) Click "Search GEO Index" button on the main page. You will have new browser with following dialog contents.





2) Type "breast cancer" keyword in the "Keyword search" field and click "Search" button, then you will have the      retrieved GDS ID info. as follows.





3) Each dataset includes the subset titles corresponding to each experimental condition. You can specify the      target and control samples by just checking the box as follows. Click "select button". It will place the specified      GSM IDs for control and target subsets on the DEG Analysis module in the main page. Then, go back to      main GS-LAGE page.






Step 2 : DEG Analysis

Click the "Search" button to execute DEG Analysis. Then, you will have a new window with the scatter plot of "GS-LAGE measures of gene expression" versus "Conventional DEG".







Step 3 : Selecting the list of Differential Expressions of Gene

There are two types of scatter plots from DEG analysis. The first plot represents the relationship between LAGE Selectivity and FOLD change. The second one represents the relationship between LAGE DEG and FOLD change.






1) You can set the cutoff values for DEG, LAGE selectivity, and LAGE DEG. Simply put each cutoff value on each text field.

2) Select one of options from each pull-down menu for filtering probes based on each cutoff value. There are two options such as "<" and ">", which correspond to the selection criteria (i.e., "less than" or "greater than" the cutoff value, respectively) for DEG, LAGE selectivity, and LAGE DEG.

3) Select one of options such as "AND" or "OR" to filter probes using logical operation as follows,

i) The selection of "AND" and "AND"

    This will select probeset, in which all probes meet the criteria such as
    [DEG value ">" cutoff value] and [LAGE selectivity ">" cutoff value] and [LAGE DEG ">" cutoff value].

ii) The selection of "OR" and "OR"

    This will select probeset, in which all probes meet the criteria such as
    [DEG value ">" cutoff value] or [LAGE selectivity ">" cutoff value] or [LAGE DEG ">" cutoff value].

iii) The selection of "AND" and "OR"

    This will select probeset, in which all probes meet the criteria such as
    [ [DEG value ">" cutoff value] and [LAGE selectivity ">" cutoff value] ] or [LAGE DEG ">" cutoff value].

iv) The selection of "OR" and "AND"

    This will select probeset, in which all probes meet the criteria such as
    [DEG value ">" cutoff value] or [ [LAGE selectivity ">" cutoff value] and [LAGE DEG ">" cutoff value] ].








4) This is the list of selected Probeset including the informaion of Gene ontology, NCBI ID, DEG, LAGE-DEG,      LAGE selectivity, gene symbol and gene description.





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