Difference between revisions of "The Class Whoopers"
From LMU BioDB 2015
Kdahlquist (Talk | contribs) (→1: paper is suitable for project) |
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*Article is available online only and LMU has paid a subscription for access to this article. | *Article is available online only and LMU has paid a subscription for access to this article. | ||
| − | === Microarray | + | === Microarray Paper === |
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This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:04, 10 November 2015 (PST)'' | This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:04, 10 November 2015 (PST)'' | ||
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* Web site where the data resides: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data] | * Web site where the data resides: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data] | ||
| − | + | <!--#2 | |
*Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11 | *Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11 | ||
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | * ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | ||
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*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | *Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | ||
| − | + | #3 | |
King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150 | King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150 | ||
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23776625 | * PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23776625 | ||
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* Web site where the data resides: [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1594/samples/?keywords=Bordetella+pertussis&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=&s_page=1&s_pagesize=100 EBI ArrayExpress Data] | * Web site where the data resides: [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1594/samples/?keywords=Bordetella+pertussis&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=&s_page=1&s_pagesize=100 EBI ArrayExpress Data] | ||
| − | + | #4 (note, all of the papers from this point on involve additional species other than Bordetella pertussis) | |
* Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785. | * Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785. | ||
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*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | *Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | ||
| − | + | #5 | |
* Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81 | * Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81 | ||
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* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/ | * Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/ | ||
| − | + | #6 | |
* Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006 | * Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006 | ||
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* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/ | * Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/ | ||
| − | + | #7 | |
*King, A. J., van Gorkom, T., Pennings, J. L., van der Heide, H. G., He, Q., Diavatopoulos, D., … Mooi, F. R. (2010). Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains. BMC Genomics, 11, 196. http://doi.org/10.1186/1471-2164-11-196 | *King, A. J., van Gorkom, T., Pennings, J. L., van der Heide, H. G., He, Q., Diavatopoulos, D., … Mooi, F. R. (2010). Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains. BMC Genomics, 11, 196. http://doi.org/10.1186/1471-2164-11-196 | ||
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* Did LMU pay a fee for this article: no | * Did LMU pay a fee for this article: no | ||
| − | + | #8 | |
*Nakamura, M. M., Liew, S.-Y., Cummings, C. A., Brinig, M. M., Dieterich, C., & Relman, D. A. (2006). Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella pertussis . Infection and Immunity, 74(10), 5537–5548. http://doi.org/10.1128/IAI.00781-06 | *Nakamura, M. M., Liew, S.-Y., Cummings, C. A., Brinig, M. M., Dieterich, C., & Relman, D. A. (2006). Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella pertussis . Infection and Immunity, 74(10), 5537–5548. http://doi.org/10.1128/IAI.00781-06 | ||
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* Publisher: Infection and Immunity | * Publisher: Infection and Immunity | ||
* Availability: online access | * Availability: online access | ||
| − | * Did LMU pay a fee for this article: no | + | * Did LMU pay a fee for this article: no!--> |
== Deliverables == | == Deliverables == | ||
Revision as of 23:51, 10 November 2015
Contents
The Class Whoopers Crew Page
The_Class_Whoopers
- Species: Bordetella pertussis
Crew Members
- Coder and Project Manager: Nicole Anguiano
- Quality Assurance: Brandon Klein
- GenMAPP Users: Lena Olufson & Mahrad Saeedi
Team Goals for the Week of 11/3
- For all:
- Make an annotated bibliography of 1-2 articles (preferably 2) on Bordetella pertussis following the instructions here, and post them on your individual journal page!
- Once everyone has done their bibliographies, we'll discuss a ranking of which we think are the best ones and list them below in ranked order. Try to find different articles from everyone else so we have the maximum number of options.
Meetings!
- Monday, November 9, 8pm, Seaver 120
Annotated Bibliography
- Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
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)
- Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11
- PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21622744
- PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147532/
- Publisher Full Text (HTML): http://jb.asm.org/content/193/15/4017.long
- Publisher Full Text (PDF): http://jb.asm.org/content/193/15/4017.full.pdf+html
- Copyright: © 2011, American Society for Microbiology (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication.
- Publisher: American Society for Microbiology (scientific society)
- Availability: in print and online
- Did LMU pay a fee for this article: no
(Note: The below paper is very similar to the genome sequencing paper listed above but more recent. We were unsure how to designate which of the two would be a better paper. If possible, feedback regarding which to choose would be appreciated. Otherwise, we would like to use the above genome sequencing paper.)
- Boinett, C. J., Harris, S. R., Langridge, G. C., Trainor, E. A., Merkel, T. J., & Parkhill, J. (2015). Complete genome sequence of Bordetella pertussis D420. Genome announcements, 3(3), e00657-15.
- The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
- The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
- The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
- The link to the full PDF version of the article from the publisher web site: http://genomea.asm.org/content/3/3/e00657-15.full.pdf+html
- The authors won't he right of the copyright under a Creative Commons license.
- The article is available "Open Access".
- Published by the American Society for Microbiology online.
- Article is available online only and LMU has paid a subscription for access to this article.
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
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)
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
