Download Expression Analysis of the Sphingolipid Metabolism

Expression Analysis of the Sphingolipid Metabolism
V
Ι
Download GenMAPP v2.1
Π
Gene Extraction:
ΙΙΙ
Data Formatting
ΙV
Download Pathways
Pathway Modification:
Branch
Addition:
Gene
Addition:
Data Application:
VΙ
I.
GenMAPP v2.1:
GenMAPP v2.1, a Windows operating program, provides a technique for conducting a genomic analysis
through the visualization of gene expression data within a metabolic pathway. Expression data derived
from microarray and other similar genomic experiments can be imported and recognized by GenMAPP
using multiple gene identifiers such as Entrez Gene, Ensembl, and Affy ID's. This program allows for
the genes within a biological pathway, such as the sphingolipid metabolism, to be color-coded based on
a profile established by the user. In addition, tools provided within GenMAPP allow such metabolic pathways
to be created or edited by the user. The figure shown below demonstrates an example of what one would obtain
after importing expression data into GenMAPP.
www.genmapp.org
II.
How to Extract Sphingolipid Related Genes:
** If desired genes have been previously extracted, proceed to step ΙΙΙ.
Perl program instructions
The perl script accepts a text file with the list of gene symbols or the tag ID’s of interest. It opens the microarray file
with normalized gene expression values and searches for rows that match with the gene symbol or Tag ID’s .The
matched rows are copied to a new test file that may be opened using excel and further data analysis can be performed.
Program Name: Affyfilter.pl
Function: Script for filtering gene expression values of interest from Normalized gene expression file
Requirement: Perl 5.8 must be down loaded and installed on the windows system from www.activestate.com without
charge. Mac ‘s have built in perl in their X11 command line.
USE: Make sure to have program file (affyfilter.pl) , genelist file and normalized microarray file in the same folder where
perl is installed.
At the command line type:
C:\ perl > perl affyfilter.pl microarray.txt genelist.txt > output.txt
The results of the filtering will be stored in a output file within the same folder (Note that the names of
the file can are user defined)
Example of a text file with gene list
Example of excel file with normalized gene expression values
III.
How to Format Data in GenMAPP
GenMAPP recognizes data to be imported in a specific format as illustrated below. Column headings:
GeneID, System Code, and a user given data heading (e.g. Control), must be included for proper
identification. The system code is a code provided by GenMAPP corresponding to the gene database used for
identifying the GeneID. The data sheet should be saved as a text document (.txt), tab-delimited file (.tab), or
comma-separated values (.csv).
Gene Identification
*Code Corresponding
to Gene Database
Data 1
System Code
Control
GeneID
54218
L
1.43
14421
L
0.51
14421
L
0.47
12091
L
2.07
- .txt, .tab, or .csv file
* System Codes:
EntrezGene:
Ensemble:
Unigene:
L
En
U
MGI:
M
UniProt: S
Affy:
X
IV.
Download Sphingolipid Pathways:
Download Sphingolipid pathways (.mapp file) from www.sphingomap.com → SphingoGeneMap and open within GenMAPP.
Available Pathways Include:
De novo
Lacto
Ganglio
Neolacto
IsoGlobo
Globo
V. How to Modify Provided Sphingolipid Pathways:
- Gene Addition
a)
b)
c)
d)
e)
Select species specific database, See Gene Database Selection
Click on gene box located in the tool bar of the draftboard
Right click gene to open “Gene Finder”
Enter the gene ID and the corresponding gene ID system
Within “Gene Label” enter gene name
V. How to Modify Provided Sphingolipid Pathways:
- Branch Addition
VI.
How to Apply Data to Pathway Using GenMAPP:
1. Gene Database Selection
a)
b)
c)
d)
Data → “Download Data from GenMAPP.org” → expand “Gene Database” and select species used
Within “Database File Name”, select database to be used and click “start”
Return to draftboard
Data → “Choose Gene Database” → select database downloaded
VI.
How to Apply Data to Pathway Using GenMAPP:
2. Creating a Color-Criteria
a)
b)
c)
d)
e)
Data → “Expression Dataset Manager”
Expression Datasets → “New Dataset” → select saved data file
Color Sets → New
Using Boolean expression values provided, establish color-criteria based on data
Save Expression File and exit “Expression Dataset Manager”
** Values in GenMAPP represent Fold Changes
Sphingolipid Metabolism
*Detailed Instructions, list of additional functions available, and downloads are
available at http://www.genmapp.org/