1. BIOL 398/S10: Bioinformatics Lab
Analyzing the Increased and Decreased Expression of Microarray Data for Vibrio cholerae
J’aime Moehlman
Amanda Wavrin
April 27th, 2010
BIOL 398/S10: Bioinformatics Lab

2. Outline
Vibrio cholerae is a waterborne disease that is infectious to humans
Statistical analysis of the microarray data
Microarray data from the Merrell et al. (2002) study
Increased expression
in microarray
Decreased expression

3. Vibrio cholerae is a waterborne disease that is infectious to humans
Organisms in the genus Vibrio are one of the most common surface water organisms in the world.
They can be found in both fresh and marine waters and live in association with other animals.
V. cholerae is noninvasive and affects the small intestine.
It produces a cholera toxin, which is responsible for the characteristic diarrhea.
This leads to dehydration, anuria, acidosis, shock, cardiac complications, and circulatory failure.

4. Microarray Analysis in the Merrel et al. study
The study was conducted in Dhaka, Bangladesh
Samples were collected from three patients.
The collected strain, O1 Inaba El Tor, was combined with an in vitro strain and used to inoculate mice.
The output ratios were corrected to represent the competitive indices (CI) of the V. cholerae.
A CI above 1 indicates increased infectivity.
A CI below 1 indicates decreased infectivity.

5. The human-shed V. cholerae had a CI above 1 indicating an enhanced infectivity.
V. cholerae that was cultured and purified in vitro did not show enhanced infectivity
RNA from each sample was used for DNA synthesis
This was labeled with Cy5 and hybridized to the microarray with a Cy3- labeled common reference strain (exponential growing).
A two-fold difference indicated differentially expressed genes

6. GenMAPP was used to download the correct V. cholerae gene database
There were 772 errors detected when converting the raw data.
We customized our data by selecting new color sets.
Pink showed increased expression
Blue showed decreased expression
Criterion 0 represented increased.
Criterion 1 represented decreased.
Statistical Criteria:
Z Score > 2
P value < 0.05
Number Changed Ranged from <3-5
% Changed Ranged < 15-25
locust names didn’t coorespond to the ones in genmapp
Data old: b/cthere was a followup study had fewer errors (updated info)

7. Increased Gene Expression for Infectivity

8. Increased Metabolic Processes and Organization resulted in more virulent strain
Amino acid
Cellular
Nitrogen
Amino Acid Processes
Are relative to cell metabolism
Movement via Flagellum
Process carried out at cellular level which controls assembly, arrangement, or disassembly of flagellum
Cellular Metabolic Process GO Term

9. Decreased Gene Expression for Infectivity

10. Decreased in Overall Organization
Nucleotide binding
Protein functions
Folding
Binding
Molecular binding
Zinc
Cation
Vitamin
Protein Folding GO Term

11. Increases in metabolic, amino acid processes and flagellum organization show overall virulence in V. cholerae
Increased metabolic processes play a role in energy distribution within the bacteria.
Increase amino acid metabolic processes present increase in storage molecules.
Increased movement via flagellum plays a role in increased overall virulence of the bacterial cells.
Amino acid processes effect protein structure, which has an overall effect on protein function.
These increases focus on the pathogenicity of V. cholerae and the structural component of the cells.

12. Decreased overall organization of the cell results in increased pathogenicity
Decreased protein binding will effect the protein structures which has an overall effect on the protein function.
Utilizes the increased storage molecules to decrease protein synthesis.
Decreases molecular binding in order to focus on increasing its’ virulence.

13. Significantly changed genes in comparison to Merrell et al. (2002)
According to the Merrell et al. study, these genes were significantly changed
VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, VCA0583
We found that only 2 of these 8 genes showed to be significantly changed in our results.
These genes were VC0647 and VCA0583
VC0647: mRNA catabolic processes, RNA processing, cytoplasm, RNA binding, 3'5'exoribonuclease activity, transferase activity, nucleotidyltransferase polyribonucleotide nucleotidyltransferase activity
VCA0583: transport, cell envelope outermembrane bounded periplasmic space, transport activity

14. References
Merrell DS, Butler SM, Qadri F, Dolganov NA, Alam A, Cohen MB, Calderwood SB, Schoolnik GK, and Camilli A. Host-induced epidemic spread of the cholera bacterium. Nature 2002 Jun 6; 417(6889)
Todar, Kenneth. Online Textbook of Bacteriology “Vibrio cholerae” bacteriology.net/cholera.html. 25 April 2010.