BIOL367/F10

BIOL/CMSI 367-01/HNRS 398-05: Biological Databases

This is the home page for the Fall 2010 Biological Databases course at Loyola Marymount University while the computer science server is down.

Announcements

Update 11/9/10: We are back using the Fall 2010 BiolDB course wiki.

You may also want to visit the Dahlquist Lab pages or the Spring 2010 Bioinformatics Lab course pages while you are here.

Week 7 In-class Exercise and Journal Assignment

Background Readings

1. Brown PO and Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999 Jan;21(1 Suppl):33-7. DOI:10.1038/4462 |

   Brown & Botstein (1999) link to full text

2. Chapter 4 of Campbell & Heyer, Discovering Genomics, Proteomics, and Bioinformatics. Available on MyLMUConnect under the "Information" section.

Overview of Microarray Data Analysis

This is a list of steps required to analyze DNA microarray data.

1. Quantitate the fluorescence signal in each spot in the microarray image.
   • Typically performed by the scanner software, although third party software packages do exist.
   • The image of the microarray slide and this quantitation are considered the "raw-est" form of the data.
   • Ideally, this type of raw data would be made publicly available upon publication.
   • In practice, the image data is usually not made available because the raw image file of one slide could be up to 100 MB in size.
   • Also, some journals do not require data deposition as a requirement for publication, so often published data are not actually available anywhere for download.
   • Microarray data is not centrally located in a single database. Some major sources are:
     • NCBI GEO
     • EBI ArrayExpress
     • Stanford Microarray Database
     • PUMAdb (Princeton Microarray Database)
     • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
2. Calculate the ratio of red/green fluorescence
3. Log₂ transform the ratios
4. Normalize the log ratios on each microarray slide
5. Normalize the log ratios for a set of slides in an experiment
6. Perform statistical analysis on the log ratios
7. Compare individual genes with known data
8. Look for patterns (expression profiles) in the data (many programs are available to do this; we won't be doing this in class)
9. Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this)
10. Map onto biological pathways (we will use GenMAPP for this)

Individual Journal Assignment

This journal entry is due on Monday, October 18 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

• Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Add the "BIOL367/F10" category to the end of your wiki page.

Preparation for Next Week's Journal Club

In preparation for the Journal Club, each individual will do the following assignment on their individual "username Week 7" pages.

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources.
2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
   • What is the importance or significance of this work?
   • What were the limitations in previous studies that led them to perform this work?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies (See Discussion).
3. Upload your completed PowerPoint slides to your journal page by the Week 7 journal deadline (you may make changes before your presentation Tuesday afternoon, but we will be evaluating the presentation you upload.)
   • For your PowerPoint presentation, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
   • The length of your presentation should be about 15 minutes.

Journal Club Articles

1. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, and Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:217. DOI:10.1186/1471-2105-8-217 |

   Salomonis et al. (2007) link to full text

2. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, and Conklin BR. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 2003;4(1):R7. DOI:10.1186/gb-2003-4-1-r7 |

   Doniger et al. (2003) link to full text

3. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, and Fraser CM. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000 Aug 3;406(6795):477-83. DOI:10.1038/35020000 |

   Heidelberg et al. (2000) link to full text

4. 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):642-5. DOI:10.1038/nature00778 |

   Merrell et al. (2002) link to full text, dataset (on this wiki)

Groups

• Rich Brous, Andrew Herman, Jennifer Okonta (3)
• Claudia Campos, Salomon Garcia, Theresa Graebner (2)
• Margie Doyle, Andrew Forney (1)
• Evan Montz, Zeb Russo (4)

Shared Journal Assignment

• Store your journal entry in the shared BIOL367/F10:Class Journal Week 7 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL367/F10" category to the end of the wiki page (if someone has not already done so).

Reflection

• How do you think biotechnology like whole genome sequencing and microarrays will affect your future?
  • How will it affect your career?
  • How will it affect your personal life?
  • What pitfalls can you forsee and how would you suggest avoiding them?
• Please feel free to respond or comment on your classmates' reflections.

Week 8 In-class Exercise and Journal Assignment

Analysis of Vibrio cholerae Microarray Data Part 1

• For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from Vibrio cholerae, and then learn how to create a Gene Database for this organism.
• The detailed instructions for the microarray data analysis we will carry out can be found on the Sample Microarray Analysis for Vibrio cholerae page.

Groups

• Rich Brous, Salomon Garcia
• Claudia Campos, Andrew Herman
• Margie Doyle, Theresa Graebener
• Andrew Forney, Zeb Russo
• Evan Montz, Jennifer Okonta

Individual Journal Assignment

This journal entry is due on Monday, October 25 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

• Store this journal entry as "username Week 8" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Add the "BIOL367/F10" category to the end of your wiki page.
• Keep an "electronic lab notebook", containing your methods, results, and interpretations of this week's portion of the Analysis of Vibrio cholerae microarray data project in your "username Week 8" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.
  • Be sure to answer any questions embedded in the protocol in your journal page.
• Upload your completed spreadsheet to your individual journal page.

Shared Journal Assignment

• Store your journal entry in the shared BIOL367/F10:Class Journal Week 8 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL367/F10" category to the end of the wiki page (if someone has not already done so).

Reflection

• What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not?
• What advice would you give next year's class when performing this assignment?
• Do you think the original authors of the Merrell et al. (2002) paper adequately discussed their methods and results of their data analysis in their Nature paper? Why or why not?

Week 9 In-class Exercise and Journal Assignment

Analysis of Vibrio cholerae Microarray Data Part 2

• For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from Vibrio cholerae, and then learn how to create a Gene Database for this organism.
• The detailed instructions for the microarray data analysis we will carry out today can be found on the GenMAPP & MAPPFinder Protocol page.

Individual Journal Assignment

This journal entry is due on Monday, November 1 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

• Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Add the "BIOL367/F10" category to the end of your wiki page.
• Keep an "electronic lab notebook", containing your methods, results, and interpretations of this week's portion of the Analysis of Vibrio cholerae microarray data project in your "username Week 9" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.
  • Be sure to answer any questions embedded in the protocol in your journal page.
• Upload and link to your completed files on your individual journal page.
  • Note that the OpenWetware wiki will not accept the upload of certain file types the GenMAPP and MAPPFinder will create. To upload these files, you will need to compress them into a .zip file, which will be accepted by this wiki.
  • The Windows machines in the Seaver 120 computer lab have an evaluation version of WinZip installed that can compress files.
  • If you are using your own Windows machine and it does not already have a program installed to compress files, the free software, 7-zip, can be downloaded and installed for you to use.

Groups

For this week, we are not going to require a face-to-face meeting of the group. However, we do strongly encourage it because answering the questions is going to require conferring with what your buddy got.

• Richard Brous (new), Zeb Russo (old) (increasing)
• Claudia Campos (new), Evan Montz(old) (decreasing)
• Margie Doyle(decreasing/new), Salomon Garcia (decreasing/old)
• Andrew Forney (old), Andrew Herman (new) (increasing)
• Theresa Graebener, Jennifer Okonta

Shared Journal Assignment

• Store your journal entry in the shared BIOL367/F10:Class Journal Week 9 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL367/F10" category to the end of the wiki page (if someone has not already done so).

Reflection

1. There has been an outbreak of cholerae in Haiti in the last week amongst the people already affected by the earthquake. For example, see the story by Partners in Health. How, specifically, do you think that research like that we are doing this week can contribute to an improvement in publich health? What do you think the barriers are for this research to lead to viable treatments that can reach the people in Haiti?
2. Next week we will be selecting the teams for the class final projects. What qualities do you look for in a good teammate? What are some of the things that make or break a team project?

Project Team Requests

• In class on November 2, the teams will be assigned for the Final Class Project.
• There will be two teams of 3 students and one team of 4 students.
• Ultimately the teams will be assigned by Drs. Dahlquist and Dionsio based on balancing areas of expertise amongst the team members. However, we would like to gather your input into the formation of the teams. At this point in the semester, you have worked with at least five other people in the class (maybe more) as buddies on journal assignments. Please send an e-mail to both Dr. Dahlquist and Dr. Dionisio by the journal deadline, midnight Monday giving us the names of two other people in the class whom you want to be on your team (you can also choose people that haven't been your journal buddy yet). Please give us a short explanation as to why you are choosing those two particular people. We will consider all team requests, but we cannot guarantee that you will be matched with both people you picked. These e-mails will remain confidential to the instructors and will not be shared with your classmates.
• Also on November 2, the species will be assigned for the Final Class Project. The assignment of species will be decided in class between the teams and the instructors after the teams have been announced. So you can start to think about it before next week, the species under consideration by the instructors are:
  • Mycobacterium smegmatis (non-pathogenic model for tuberculosis that is being studied by the freshmen HHMI lab class)
  • Helicobacter pylori (gut bacterium that causes stomach ulcers in humans)
  • Salmonella typhimurium (pathogen responsible for food-borne illness and egg recalls)
• You may propose a different species than one of the above, as long as it fulfills the following criteria:
  1. The genome is completely sequenced and has been published in a journal article
  2. The complete proteome set of data (UniProt XML and GOA) are available through the Integr8 database.
  3. At least one DNA microarray dataset has been performed on this species, the data has been published in a journal article, and the complete dataset is publicly available and uses an ID system present in the UniProt XML. Sources of DNA microarray data include:
     • NCBI GEO
     • EBI ArrayExpress
     • Stanford Microarray Database
     • PUMAdb (Princeton Microarray Database)
     • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.