Rlegaspi Week 15

Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

• Coder: Mary Alverson
• GenMAPP User & Project Manager: Ron Legaspi
• Quality Assurance: Josh Kuroda
• GenMAPP User: Emily Simso

Important Links

Our Deliverables

Gene Database Project Links
Overview	Deliverables	Reference Format	Guilds	Project Manager	GenMAPP User	Quality Assurance	Coder
			Teams	Heavy Metal HaterZ	The Class Whoopers	GÉNialOMICS	Oregon Trail Survivors

Individual Journal Entries
Mary Alverson	Week 11	Week 12	Week 14	Week 15
Emily Simso	Week 11	Week 12	Week 14	Week 15
Ron Legaspi	Week 11	Week 12	Week 14	Week 15
Josh Kuroda	Week 11	Week 12	Week 14	Week 15

Goals for Week 15

Data Preparation and Statistical Analysis for GenMAPP

1. Consult with Dr. Dahlquist on how to process the data (normalization, statistics)
2. Perform the statistical analysis in Excel.
3. Format the gene expression data for import into GenMAPP.

*Similar to goals from Week 14.

Summary of Progress and Procedure

Compiling Raw Data and Statistical Analysis

December 8, 2015

• Calculated averages from the split data
  • Discovered that there are a total of 5408 genes.
• Calculated biological averages of each time point
• Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
  • Subtracted not divided due to log space
• Performed TTest on the above relationships to get the Pvalue
• Performed Bonferroni
• Performed Benjamini & Hochberg
• Excel file after all of these procedures were uploaded to XMLPipeDB and link to file is as follows: File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx

External Links

Ron Legaspi
BIOL 367, Fall 2015

Assignment Links

• Week 1 Assignment
• Week 2 Assignment
• Week 3 Assignment
• Week 4 Assignment
• Week 5 Assignment
• Week 6 Assignment
• Week 7 Assignment
• Week 8 Assignment
• Week 9 Assignment
• Week 10 Assignment
• Week 11 Assignment
• Week 12 Assignment
• Week 14 Assignment
• Week 15 Assignment

Individual Weekly Journals

• Individual Journal Week 1 - This is my User Page
• Individual Journal Week 2
• Individual Journal Week 3
• Individual Journal Week 4
• Individual Journal Week 5
• Individual Journal Week 6
• Individual Journal Week 7
• Individual Journal Week 8
• Individual Journal Week 9
• Individual Journal Week 10
• Individual Journal Week 11
• Individual Journal Week 12
• Individual Journal Week 14
• Individual Journal Week 15

Shared Weekly Journals

• Shared Journal Week 1
• Shared Journal Week 2
• Shared Journal Week 3
• Shared Journal Week 4
• Shared Journal Week 5
• Shared Journal Week 6
• Shared Journal Week 7
• Shared Journal Week 8
• Shared Journal Week 9
• Heavy Metal HaterZ Team Page - Week 10-15 Shared Journal