Week 2

Team Information & Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

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

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein	Week 11	Week 12	Week 14	Week 15
Lena Olufson	Week 11	Week 12	Week 14	Week 15
Mahrad Saeedi	Week 11	Week 12	Week 14	Week 15
Team Entries	Week 11	Week 12	Week 14	Week 15

Group Members

• Project Manager & Coder: Brandon Klein
• Quality Assurance: Mahrad Saeedi
• GenMAPP User: Lena Olufson
• Team Page

Team Weekly Assignments

• Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
• Week 11 (midnight 11/17)
• Week 12 (midnight 11/24)
• Week 14 (midnight 12/8)
• Week 15 (midnight 12/15)

Weekly Updates

Week 11

Goals

• For all:
  • Outline your assigned paper on your user page and include a list of 10 defined terms from the paper.
• Nicole & Brandon
  • Prepare Journal Club presentation on the designated genome sequencing article
  • Slides Due: by midnight, Tuesday, November 17
  • Presentation Date: Tuesday, November 24
• Lena & Mahrad
  • Prepare Journal Club presentation on the designated microarray paper
  • Slides Due: by midnight, Tuesday, November 17
  • Presentation Date: Tuesday, November 17

Progress

• Nicole Anguiano (Coder):
• Brandon Klein (QA):
• Lena Olufson (GennMAPP):
• Mahrad Saeedi (GennMAPP):

Meetings!

• TBD

Week 10

Goals

• For all:
  • Create an annotated bibliography including one genome sequencing paper and two microarray experiments for Bordetella pertussis
  • Create/update team page & compile group annotated bibliography
  • Assignment due date: Midnight Tuesday, November 10

Progress

• All group members created annotated bibliographies and compiled them on the newly created group page.

Meetings!

• Monday, November 9, 8pm-9pm, Seaver 120

Deliverables

• GenMAPP Gene Database for assigned species (.gdb)
• ReadMe file to accompany the Gene Database (.pdf)
• Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
• Include Gene Database Schema diagram in ReadMe
• Sample schema in Adobe Illustrator format: Vibrio_schema_20101022.zip
• Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)
• Processed and analyzed DNA microarray dataset (.xls)
• GenMAPP Expression Dataset file (.gex)
• Filtered MAPPFinder Results (.xls)
• Sample MAPP file of a relevant biological pathway for your species (.mapp)
• Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
• PowerPoint presentation (.ppt, given on Tuesday, December 15)

Annotated Bibliography

Genome Sequencing Paper

Neither of these papers is the first to report the genome sequence of B. pertussis. The paper that you will want to use is this one. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. — Kdahlquist (talk) 09:54, 10 November 2015 (PST)

Note: revise/complete this citation

• Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
• PubMed Central: Not available on PubMed Central
• Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
• Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
• Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication
• Publisher: Nature Publishing Group (for profit?)
• Availability: in print and online
• Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal Nature Genetics.

Microarray Paper

This paper is suitable for your project. — Kdahlquist (talk) 10:04, 10 November 2015 (PST)

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264864/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0115243&representation=PDF
• Copyright: © 2014 Hoo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. (info found here)
• Publisher: PLOS ONE (respected open access organization)
• Availability: online only
• Did LMU pay a fee for this article: no
• Web site where the data resides: NCBI GEO data