Ksherbina Week 10

Katrina Sherbina

Class Page    User Page

Assignment Description

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 15

Class Journal

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Individual Journal

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Other

Week 5: Database Wiki

Final Project

Team H(oo)KD Project Page

Journal Club Presentation

Project Individual Journal

Locate journal article describing C. trachomatis reference genome

1. Go to the PubMed site through the link provided in the LibGuide for the class.
2. Beneath the search bar at the top of the page, click on the "Advanced" link.
3. Create filters for the search:
   • In the first blank field, type in the species name: Chlamydia trachomatis.
   • In the drop down menu to the left of that first field, select "MeSH Terms".
   • In the next blank field, type in the term "genome".
   • In the drop down menu to the left of this field, select "Title".
   • Click on the "Search" button to search for an article satisfying the filters that were set.
4. Go to the last page of the search results. Since you are looking for the first description of the reference genome for the species of interest, the journal article you are looking for will probably be one of the older articles that come up in the search.
   • Reference genome article for C. trachomatis: Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L.,... Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282: 754-759.
5. Click on the link of an article that seems promising. If, after reading the abstract, you believe that this is the article that you are looking for, click on one of the links in the top right under "Links to full text" to retrieve the full article.
6. Go to the Web of Science database through the link provided in the LibGuide for the class.
7. In the first blank search field, type in part of the title of the article about the reference genome.
   • For the article aforementioned, I typed in "obligate intracellular pathogen".
8. In the drop down menu to the right, select "Title".
9. In the next blank search field, type in the author's name.
   • For the article aforementioned, I typed in "Stephens".
10. Click on the "Search" button. One of the results should be the article that you found on the reference genome.
11. In the citation for the result that matches the title of the article about the reference genome, click on the link that designates the number of times that the article was cited.

Locate journal articles that measure gene expression

Locating microarray data on EBI ArrayExpress

1. Go to the EBI ArrayExpress database.
2. Click on "Experiments" in the navigation toolbar toward the top of the website.
3. Go to the "By organism" drop down menu in the "Filter Experiments" section. Select the species Chlamydia trachomatis.
4. Click on the "Filter" button to locate the microarray datasets on the database for the selected species.
5. Click on one of the links in the "Accession" column to go to the page in the database that contains the microarray data for the experiment designated by that accession number. You will be taken to a site that has a table of various information.
   • For example, click on the link "E-GEOD-10199". This takes you to a page titled "E-GEOD-10199 - Glycogen Accumulation in Chlamydia trachomatis is Controlled by its Plasmid Through Regulation of glgA".
   • Note: The data under the accession number E-GEOD-24119 has not been published in a journal.
6. Scroll down to the last row of the table with the designation "Links". Click on the first link in the row, which is in the format "GEO - GSE10199". This will take you to a page on the NCBI GEO database, which will contain the citation for the article published regarding the data (if an article was published).
   • For the page opened by clicking on the accession number "E-GEOD-10199", click on the link "GEO - GSE10199" in the "Links" row.
7. Copy and Paste the name of the article listed in the citation into the search field in Google Scholar.
   • For instance, the name of the journal article corresponding to the data with the aforementioned accession number is "The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factor".
8. Click on the link in the search results that matches the name of the article. This will take you to the site that contains the article.

Locating journal articles published on microarray datasets not in EBI ArrayExpress

1. Go to the PubMed site through the link provided in the LibGuide for the class.
2. Beneath the search bar at the top of the page, click on the "Advanced" link.
3. Create filters for the search:
   • In the first blank field, type in the species name: Chlamydia trachomatis.
   • In the drop down menu to the left of that first field, select "MeSH Terms".
   • In the next blank field, type in the term "microarray".
   • In the drop down menu to the left of this field, select "Title/Abstract".
4. Click on the "Search" button to search for articles meeting the filter criteria.
   • Note: None of the articles that appeared in the results included microarray data that will work for this project either as supplementary material or in an external database. Some of the papers used human microarrays while other papers that used C. trachomatis arrays did not give information about accessing the raw microarray data.
5. Find the reference genome article for the species in the Web of Science as specified in the section Locate journal article describing C. trachomatis reference genome.
6. In the citation for the article, click on the link for the number of times that article was cited by other articles.
7. In the "Refine results" section to the left, type in "microarray" in the field beneath "Search within results for". Then, click on the "Search" button.
   • Note: As with the search performed in PubMed, none of the articles were in the results of the search were suitable for this project. Either the paper described an experiment using human microarrays or the actual raw microarray data could not be found.