1. GenoCMS Gene-centric Content Management System Catalogue for Human Chromosome 18. Quick Start Guide © PostgenTech © ProContent

2. Typical workflow consists of seven steps © PostgenTech © ProContent

3. Demo scenario Task: select a set of the salient genes, potentially relevant as cancer biomarkers  Log in as Guest  View default proteins set  Change display settings  Select proteins to a new User Set  Delete proteins from the User Set  Table view  Export data  Registration and login  Share the User Set © PostgenTech © ProContent

4. Log in as Guest Use one of Guest login hyperlinks from the front page to start working with the system (shown green arrows). © PostgenTech © ProContent

5. View default proteins set After selecting Guest Login the default set of proteins is loaded into the current Workspace. Set name and description © PostgenTech © ProContent

6. Change display settings To change the composition of the visible tracks switch to the “Descriptors” tab. Tracks Protein names © PostgenTech © ProContent

7. Change display settings The currently visible tracks are marked by the green color of the check sign. Click the “Reset settings”. Search relevant tracks Remove settings by one click Track categories © PostgenTech © ProContent

8. Change display settings Make sure that the settings are reset. Input to Quick search “ HepG2_iBAQ “(shown green arrows). © PostgenTech © ProContent

9. Change display settings Select the track by clicking the grey check sign to include it into the matrix browsing. Make sure that the check sign is green. So you choose the track for protein abundance (iBAQ index) in the HepG2 cell line. Do the same for track “ Liver_RNASeq ” (transcript abundance (RPKM) in liver tissue). Return to “Proteins” tab. © PostgenTech © ProContent

10. Select proteins to a new User Set Click to sort the map according to the “ HepG2_ iBAQ ” track. Use “on mouse over” tooltip to find it. Tooltip © PostgenTech © ProContent

11. Select proteins to a new User Set Select genes/proteins that are differentially expressed in HepG2 and liver tissue. These are visualized with a discrepancy in the colors of the neighboring panels. The information about the sorted track © PostgenTech © ProContent

12. Select proteins to a new User Set Click, then select “Add new set” checkbox and finish with “Add to set” button. © PostgenTech © ProContent

13. Select proteins to a new User Set Fill the form and click “Save”. You will be redirect to your new set. © PostgenTech © ProContent

14. Delete proteins from the User Set To change the composition of the visible tracks switch to the “Descriptors” tab. Select the tracks to include it into the matrix browsing:  nd_MSPR (normalized number of observations in MS experiments);  Cancer (proportional to number of papers supporting gene association with cancer);  Dr (number of diseases associated with protein). And switch to “Descriptors” >> “Descriptors' setting”. © PostgenTech © ProContent

15. Delete proteins from the User Set Switch-on toggle for separator after “ Liver_RNASeq ” track. Make sure that the check sign is green. You may change tracks order if it is necessary. Return to “Proteins” tab. Change tracks order © PostgenTech © ProContent

16. Delete proteins from the User Set Sort the map according to the “ nd_MSPR ” track. Select genes/proteins that have lowest values. Click, then confirm deletion. Separator Select all in column Quick link to Descriptors' setting © PostgenTech © ProContent

17. Table view The matrix view can be switch to the tabular format selecting the “Table” hyperlink at the upper toolbar. Color scheme of some tracks depends on set © PostgenTech © ProContent

18. Table view To change visibility and order of the protein names switch to “Descriptors” >> “Identifiers’ setting”. Separator © PostgenTech © ProContent

19. Table view Change identifiers order Switch-off toggle for name “ UniProt AC ”. Switch-on toggle for name “ Gene ”. You may change identifiers order if it is necessary. Return to “Proteins” tab. © PostgenTech © ProContent

20. Export data The relevance of the differentially expressed genes to cancer is shown for 3 genes: SLC39A6, MIB1, MALT1. To export the created set use. Sorting Tooltip © PostgenTech © ProContent

21. Registration and log in To share your work you have to register and log in. Use “Register” or “Sign up” hyperlink from the front page of the GenoCMS. In the form of registration you need to fill your e-mail, user name and password and click “Sign up”. After registration you can authorize in the system by using hyperlink “Login”. © PostgenTech © ProContent

22. Share the User Set If you have passed registration in the same day from the same computer, the set, created under Guest account, will be automatically linked with your new account. To find your set switch to “Sets” >> “My sets”. Use to enter in edit mode. © PostgenTech © ProContent

23. Share the User Set Toggle the checkbox “Shared” and save changes. In result the set will be available among the users of one GenoCMS server. © PostgenTech © ProContent

24. Thank You The set, received by using this presentation, may be different from shown at images, since the data is constantly updated. For more information download Quick Start Guide from the front page of the GenoCMS. © PostgenTech © ProContent