Quick start guide

GenoCMS Gene-centric Content Management System

Catalogue for Human Chromosome 18.

Quick Start Guide

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Typical workflowconsists of seven steps


Demo scenarioTask: 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


Log in as Guest

Use one of Guest login hyperlinks from the front page to start working with the system (shown green arrows).


View default proteins set

After selecting Guest Login the default set of proteins is loaded into the current Workspace.

Set name and description


Change display settings

To change the composition of the visible tracks switch to the “Descriptors” tab.

Tracks

Protein names



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



Make sure that the settings are reset. Input to Quick search “HepG2_iBAQ “(shown green arrows).



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.


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



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



Click , then select “Add new set” checkbox and finish with “Add to set” button.



Fill the form and click “Save”. You will be redirect to your new set.


Delete proteins from the User SetTo 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”.


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


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


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


Table view

To change visibility and order of the protein names switch to “Descriptors” >> “Identifiers’ setting”.

Separator


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.


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


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”.


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.


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.


Thank YouThe 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.


Quick start guide

Education

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