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:

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:

[[File:Samplegenemapp.png]]

*[[File:Samplegenemapp.png]]

*Gene IDs:

*Gene IDs:

** '''bp1123''' refers to the OrderedLocusNames gene ID system.

** '''bp1123''' refers to the OrderedLocusNames gene ID system.

===Creating an Expression Dataset in the Expression Dataset Manager===

===Creating an Expression Dataset in the Expression Dataset Manager===

The file [[[[File:Bpertussis compiledrawdata cw20151208.txt]]]] was used to create an expression dataset in GenMAPP.

The file [[File:Bpertussis compiledrawdata cw20151208.txt]] was used to create an expression dataset in GenMAPP.

*Total Number of Gene IDs Imported

*Total Number of Gene IDs Imported

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

#*We 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.

#*We 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_ABC_Samples] > 0.25 AND [Pvalue] < 0.05</code>.

#*We stated the criterion as follows and added it to the Criteria List: <code>[Avg_ABC_Samples] > 0.25 AND [B-H_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, we 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.

#*We 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".

#*We 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.

#*We 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_ABC_Samples] < -0.25 AND [Pvalue] < 0.05</code>

#*We stated the criterion as follows and added it to the Criteria List: <code>[Avg_ABC_Samples] < -0.25 AND [B-H_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, 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.

Screenshot of Color Set criteria:

Screenshot of Color Set criteria:

*[[File:Expressioncolorset.png]]

*[[File:Expression dataset BHpvalue criteria.png]]

Note: No errors were encountered in the creation of the Color Set.

Note: No errors were encountered in the creation of the Color Set.

** Then, we searched our organism in the drop down menu at the top of the page, and we selected the Bordetella pertussis Tomaha I organism, and clicked "Go".

** Then, we searched our organism in the drop down menu at the top of the page, and we selected the Bordetella pertussis Tomaha I organism, and clicked "Go".

** This lead us to a page of the ribosome pathway with the gene IDs that pertained to our specific organism. We were then able to create a mapp using these genes in GenMAPP.

** This lead us to a page of the ribosome pathway with the gene IDs that pertained to our specific organism. We were then able to create a mapp using these genes in GenMAPP.

** Each of the green highlighted genes on the ribosome pathway were entered into the GenMAPP mapp by entering each gene ID and the name given from the Kegg pathway, and then the expression dataset "bpertussis_expressiondataset_cw20151213" was applied to the genes to color code them.

** Each of the green highlighted genes on the ribosome pathway were entered into the GenMAPP mapp by entering each gene ID and the name given from the Kegg pathway, and then the expression dataset "bpertussis_expressiondataset_cw20151218" was applied to the genes to color code them.

**Here is the screenshot of the final mapp for the ribosome pathway created:

**Here is the picture of the final mapp for the ribosome pathway created:

* [[File:RibosomeGenMAPP.png]]

*[[File: Bpertussis ribosomepathway cw20151218.jpg]]

** Most of the ribosome genes that were generated on this mapp appeared to be the color green, symbolizing a decrease, except for the grey colored genes that were not significantly changed in this experiment. Since the genes mapped for the ribosome pathway all appeared to be green, this means that the expression levels of the genes pertaining to the ribosome category all decreased during the microarray experiment. Ribosomes play a key role in the translation process in cells and without them genes are often repressed and unable to perform their proper functions as they are unable to complete the replication processes. The microarray experiment analysis revealed that the absence of a membrane-associated protein named KpsT in B. pertussis, resulted in global down-regulation of gene expression including key virulence genes. The ribosome pathway depicted genes that were decreasing in gene expression, thus linking the translation process to the down-regulated key genes from the experiment because since these genes were lacking a necessary protein to help them perform the proper replication processes, translation did not occur in these genes and thus the ribosomes were not involved, ultimately leading to the decrease in expression of the genes mapped in the ribosome pathway.

** Most of the ribosome genes that were generated on this mapp appeared to be the color green, symbolizing a decrease, except for the grey colored genes that were not significantly changed in this experiment. Since the genes mapped for the ribosome pathway all appeared to be green, this means that the expression levels of the genes pertaining to the ribosome category all decreased during the microarray experiment. Ribosomes play a key role in the translation process in cells and without them genes are often repressed and unable to perform their proper functions as they are unable to complete the replication processes. The microarray experiment analysis revealed that the absence of a membrane-associated protein named KpsT in B. pertussis, resulted in global down-regulation of gene expression including key virulence genes. The ribosome pathway depicted genes that were decreasing in gene expression, thus linking the translation process to the down-regulated key genes from the experiment because since these genes were lacking a necessary protein to help them perform the proper replication processes, translation did not occur in these genes and thus the ribosomes were not involved, ultimately leading to the decrease in expression of the genes mapped in the ribosome pathway.

** Then, we searched our organism in the drop down menu at the top of the page, and we selected the Bordetella pertussis Tomaha I organism, and clicked "Go".

** Then, we searched our organism in the drop down menu at the top of the page, and we selected the Bordetella pertussis Tomaha I organism, and clicked "Go".

** This lead us to a page of the nitrogen metabolism pathway with the gene IDs that pertained to our specific organism. We were then able to create a mapp using these genes in GenMAPP.

** This lead us to a page of the nitrogen metabolism pathway with the gene IDs that pertained to our specific organism. We were then able to create a mapp using these genes in GenMAPP.

** Each of the green highlighted genes on the nitrogen metabolism pathway were entered into the GenMAPP mapp by entering each gene ID and the name given from the Kegg pathway, and then the expression dataset "bpertussis_expressiondataset_cw20151213" was applied to the genes to color code them.

** Each of the green highlighted genes on the nitrogen metabolism pathway were entered into the GenMAPP mapp by entering each gene ID and the name given from the Kegg pathway, and then the expression dataset "bpertussis_expressiondataset_cw20151218" was applied to the genes to color code them.

** Here is the screenshot of the final mapp for the nitrogen cycle pathway created:

** Here is the picture of the final mapp for the nitrogen cycle pathway created:

* [[File:NitrogencycleGenMAPP.png]]

*[[File:Finalnitrogencyclebpertussis cw20151218.jpg]]

** This mapp displayed both red and green colored genes; the green highlighted genes symbolizing a decrease and the red highlighted genes symbolizing an increase, as well a couple of gray genes that were not significant to the criterion. This nitrogen cycle mapp was created due to the important metabolic processes that occur in order to keep cells alive and reproducing, and specifically the nitrogen metabolism cycle. The genes that displayed red in this mapp had increased expression during the microarray experiment, and from the kegg pathway given for nitrogen metabolism, these genes can be seen to specifically aid in the metabolism of glutamate. Glutamate is important to cells as it plays a role in providing energy to allow the cells to operate correctly, and since the glutamate-related genes that we mapped were increased, it can be determined that glutamate plays a role in supplying the underlying energy to allow for the Bordetella pertussis strains to produce the polysaccharide capsule transport proteins, as studied in the microarray experiment.

** This mapp displayed both red and green colored genes; the green highlighted genes symbolizing a decrease and the red highlighted genes symbolizing an increase, as well a couple of gray genes that were not significant to the criterion. This nitrogen cycle mapp was created due to the important metabolic processes that occur in order to keep cells alive and reproducing, and specifically the nitrogen metabolism cycle. The genes that displayed red in this mapp had increased expression during the microarray experiment, and from the kegg pathway given for nitrogen metabolism, these genes can be seen to specifically aid in the metabolism of glutamate. Glutamate is important to cells as it plays a role in providing energy to allow the cells to operate correctly, and since the glutamate-related genes that we mapped were increased, it can be determined that glutamate plays a role in supplying the underlying energy to allow for the Bordetella pertussis strains to produce the polysaccharide capsule transport proteins, as studied in the microarray experiment.

*MAPPFinder Analysis Results

*MAPPFinder Analysis Results

**We selected "Show Ranked List" to see a list of the most significant Gene Ontology terms. A screenshot of this output is shown below:

**We selected "Show Ranked List" to see a list of the most significant Gene Ontology terms. A screenshot of this output is shown below:

**[[File:Mappfinderrankedlist.png]]

**[[File:GeneontologyresultsBHpvalue.png]]

***The majority of the most significant gene ontology terms pertained to ribosome biosynthesis and translation.

***The majority of the most significant gene ontology terms pertained to ribosome biosynthesis and translation.

=== Compare Gene Database to Outside Resource===

=== Compare Gene Database to Outside Resource===