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GenoCMS
Gene-centric Content
Management System
Catalogue for Human Chromosome 18.
Quick Start Guide
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Typical workflow
consists of seven steps
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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
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Log in as Guest
Use one of Guest login hyperlinks from the front page
to start working with the system (shown green arrows).
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View default proteins set
Set name and
description
After selecting Guest Login the default set of proteins
is loaded into the current Workspace.
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Change display settings
Tracks
Protein names
To change the composition of the visible tracks
switch to the “Descriptors” tab.
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Change display settings
Remove settings by one click
Track categories
Search relevant tracks
The currently visible tracks are marked by the green
color of the check sign . Click the “Reset settings”.
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Change display settings
Make sure that the settings are reset. Input to Quick
search “HepG2_iBAQ “(shown green arrows).
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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.
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Select proteins to a new User Set
Tooltip
Click to sort the map according to the “HepG2_
iBAQ” track. Use “on mouse over” tooltip to find it.
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Select proteins to a new User Set
The information about the sorted track
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.
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Select proteins to a new User Set
Click
, then select “Add new set” checkbox and
finish with “Add to set” button.
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Select proteins to a new User Set
Fill the form and click “Save”. You will be redirect to
your new set.
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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”.
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Delete proteins from the User Set
Change tracks order
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.
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Delete proteins from the User Set
Select all in column
Quick link to
Descriptors' setting
Separator
Sort the map according to the “nd_MSPR” track.
Select genes/proteins that have lowest values.
Click
, then confirm deletion.
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Table view
Color scheme of some
tracks depends on set
The matrix view can be switch to the tabular format
selecting the “Table” hyperlink at the upper toolbar.
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Table view
Separator
To change visibility and order of the protein names
switch to “Descriptors” >> “Identifiers’ setting”.
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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.
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Export data
Tooltip
Sorting
The relevance of the differentially expressed genes to
cancer is shown for 3 genes: SLC39A6, MIB1, MALT1.
To export the created set use .
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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”.
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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.
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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.
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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.