Cell Illustrator

Gene Net Mode

Reference Manual

 

 

 

 

 

 

 

 

 

 

 

© 2002-2007 GNI Ltd.

All rights reserved.


Table of contents:

1      Introduction.. 4

2      Glossary.. 5

3      Gene Net Mode.. 6

3.1       Switching to the Gene Net Mode. 6

3.2       Differences between Gene Net and Biopathway Modeling Modes. 7

3.3       Documentation for Biopathway Modeling Mode. 8

4      Workspace in the Gene Net Mode.. 9

4.1       Menu Bar Commands. 10

4.2       CI Toolbars. 41

5      Drawing Canvas.. 45

5.1       Canvas Popup Menus. 45

6      Element Lists.. 47

7      Element Settings.. 49

7.1       Model and Canvas Property Sheet. 49

7.2       Gene Property Sheets. 49

7.3       Edge Property Sheets. 50

8      Preferences.. 52

9      Graph Layout.. 53

9.1       Graph Layout Algorithms. 54

10        Keyword Search.. 55

11        Pathway Search.. 57

11.1    Search From Combo Box. 57

11.2    Search to Combo Box. 58

11.3    Show Probe ID.. 58

11.4    Number of Edges. 58

11.5    Direction Combo Box. 58

11.6    Passing Genes. 58

11.7    Add Results to Current Subnet 58

11.8    Execute Button. 59

12        Pathway Search Results.. 60

13        Subnets.. 61

14        Gene List Search.. 63

15        Expression Plot.. 65

16        Partial Residual Plot.. 66

17        Gene Mining.. 67

17.1    Gene List 68

17.2    Gene Info. 68

17.3    Gene Pubmed. 68

17.4    Link Summary. 68

17.5    PubMed Links. 69

17.6    KEGG Link. 69

17.7    MIM Links Panel 69

17.8    Refresh Button. 69

18        Print Model.. 70

19        External References.. 71

20        Add/Edit References.. 72

21        Save Dialog.. 73

22        About Cell Illustrator.. 74