=12/13/15=

=12/13/15=

* The above steps were repeated due to the creation of a new .gdb file by the Coder. Once downloading the ________ file, I ran it through the

* The above steps were repeated due to the creation of a new .gdb file by the Coder. Once downloading the bpertussis-std_cw20151210.gdb file, I obtained the new .txt file and then prepared to import into GenMAPP.

==bpertussis-std_cw20151210.gdb Use in GenMAPP==

==bpertussis-std_cw20151210.gdb Use in GenMAPP==

===Putting a Gene on the MAPP Using the GeneFinder Window===

===Putting a Gene on the MAPP Using the GeneFinder Window===

We made a sample MAPP in which gene IDs conforming to the naming conventions of the 5 major gene databases containing ''Bordetella pertussis'' genome data were added. A screenshot of the resulting MAPP is provided below:

I made a sample MAPP in which gene IDs conforming to the naming conventions of the 5 major gene databases containing ''Bordetella pertussis'' genome data were added. A screenshot of the resulting MAPP is provided below:

[[File:Samplegenemapp.png]]

[[File:Samplegenemapp.png]]

*Gene IDs:

*Gene IDs:

**There were 341 exceptions during the creation of the expression dataset. A screenshot of the error message is shown here:  

**There were 341 exceptions during the creation of the expression dataset. A screenshot of the error message is shown here:  

***[[File:Errors in genmapp.png]]

***[[File:Errors in genmapp.png]]

===Coloring a MAPP with Expression Data===

===Coloring a MAPP with Expression Data===

====Creating a New Color Set====

====Creating a New Color Set====

We customized the new Expression Dataset by creating a new color set entitled "LogFoldChange".

# I customized the new Expression Dataset by creating a new color set entitled "LogFoldChange".

# We created a criterion for this color set to label genes that demonstrated a significant ''increase'' in their expression.

# I created a criterion for this color set to label genes that demonstrated a significant ''increase'' in their expression.

#*We specified the gene value as "Avg_ABC_Samples" for the ''Bordetella pertussis'' microarray dataset.

#*I specified the gene value as "Avg_ABC_Samples" for the ''Bordetella pertussis'' microarray dataset.

#*We activated the ''Criteria Builder'' by clicking the ''New'' button and named the criterion "Increased".

#*I activated the ''Criteria Builder'' by clicking the ''New'' button and named the criterion "Increased".

#*We selected the color for this criterion as red using the color box.

#*I selected the color for this criterion as red using the color box.

#*We stated the criterion as follows and added it to the Criteria List: <code>[Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05</code>.

#*I stated the criterion as follows and added it to the Criteria List: <code>[Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05</code>.

#Second, we created a criterion for this color set to label genes that demonstrated a significant ''decrease'' in their expression.

#Second, I created a criterion for this color set to label genes that demonstrated a significant ''decrease'' in their expression.

#*We specified the gene value as "Avg_ABC_Samples" for the ''Bordetella pertussis'' microarray dataset.

#*I specified the gene value as "Avg_ABC_Samples" for the ''Bordetella pertussis'' microarray dataset.

#*We activated the ''Criteria Builder'' by clicking the ''New'' button and named the criterion "Decreased".

#*I activated the ''Criteria Builder'' by clicking the ''New'' button and named the criterion "Decreased".

#*We selected the color for this criterion as green using the color box.

#*I selected the color for this criterion as green using the color box.

#*We stated the criterion as follows and added it to the Criteria List: <code>[Avg_LogFC_all] < -0.25 AND [Pvalue] < 0.05</code>

#*I stated the criterion as follows and added it to the Criteria List: <code>[Avg_LogFC_all] < -0.25 AND [Pvalue] < 0.05</code>

# Upon entering these color sets, we saved the entire Expression Dataset by selecting Save from the Expression Dataset menu. This effectively updated our .gex file with the new Color Set.

# Upon entering these color sets, I saved the entire Expression Dataset by selecting Save from the Expression Dataset menu. This effectively updated my .gex file with the new Color Set.

Screenshot of Color Set criteria:

Screenshot of Color Set criteria:

====Creating a Pathway-Based MAPP Using Colored Genes====

====Creating a Pathway-Based MAPP Using Colored Genes====

====Ribosome Kegg Pathway====

====Ribosome Kegg Pathway====