Blitvak Week 10 - Revision history

Blitvak: added extra bullet

2015-11-10T06:08:04Z

added extra bullet

Blitvak: some minor edits regarding the microarray results

2015-11-10T06:07:10Z

some minor edits regarding the microarray results

Blitvak: added numbering for the bib. entries

2015-11-10T05:47:23Z

added numbering for the bib. entries

@@ Line 38: / Line 38: @@
 #* How many articles does this article cite: 150
 #* How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
 #Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.
 #* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946

@@ Line 9: / Line 9: @@
 *'''Web of Science''' was entered, on 11/8, and a search was conducted using the keywords <code>Burkholderia cenocepacia genome</code> via  search by ''Topic''; this search yielded '''104 results''' (93 articles and 9 review papers out of the 104). Adding the keywords <code>nucleotide sequence</code> led to there being '''8 results''' (genome paper on the J2315 strain was the first result).
 ===Advanced Searches===
-*'''Pubmed''' was entered on 11/9 and an advanced search was conducted using <code>((((genome[Title/Abstract]) AND burkholderia cenocepacia[Text Word]) AND J2315[Text Word]))</code>; it was decided that the strain of focus will be J2315 and, thus, ''J2315'' was searched for through the use of the ''[Text Word]'' advanced search field. It was also determined that the word ''genome'' would go well with the ''[Title/Abstract]'' (it was thought that this will would make the results focus on genomes and genome-related experimental work). ''Burkholderia Cenocepacia'' was also used with the ''[Text Word]'' field. In the end, this advanced search led to ''25 results'', with one of the results being a genome paper on J2315 (the rest being research that, presumably, stemmed from that work).
+*'''Pubmed''' was entered on 11/9 and an advanced search was conducted using <code>((((genome[Title/Abstract]) AND burkholderia cenocepacia[Text Word]) AND J2315[Text Word]))</code>; it was decided that the strain of focus will be J2315 and, thus, ''J2315'' was searched for through the use of the ''[Text Word]'' advanced search field. It was also determined that the word ''genome'' would go well with the ''[Title/Abstract]'' (it was thought that this will would make the results focus on genomes and genome-related experimental work). ''Burkholderia Cenocepacia'' was also used with the ''[Text Word]'' field. In the end, this advanced search led to '''25 results''', with one of the results being a genome paper on J2315 (the rest being research that, presumably, stemmed from that work).
 *'''Google Scholar''' was entered on 11/9 and an initial search was conducted with <code>burkholderia cenocepacia genome j2315</code>, this led to '''about 933 results''' with the top result being the genome paper of interest (''The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients''); the rest of the papers, as was previously seen, were related to work tied to the genome of the bacteria. The advanced search menu item was clicked (by pressing the arrow button to the right of the ''My Citations'' menu item) and the advanced search overlay popped up; I decided to work with the ''where my words occur'' section and I changed the setting to ''in the title of the article''. Using the advanced search <code>allintitle: burkholderia cenocepacia genome j2315</code>, I found '''7 results''' and the genome paper of choice was the top result.
 *'''Web of Science''' was entered on 11/9 and ''Basic Search'' was set to ''Advanced Search'' through the drop-down menu next to the Basic Search heading. I noticed that there was a little help section next to the search box which listed the Booleans and Field Tags that can be used. I decided to use the TS (topic), TI (title, and the AND boolean; I used <code>TS=(burkholderia cenocepacia AND J2315 AND cystic fibrosis) AND TI=(genome)</code> for my advanced search which led to '''6 results''', which included the genome paper of interest.
 ===Prospective Search===
 *Web of Science was entered on 11/9/15
@@ Line 22: / Line 21: @@
 *Database Used: [http://www.ebi.ac.uk/arrayexpress/help/how_to_search.html#AdvancedSearchExperiment ArrayExpress]
 *Search was initially conducted by using these keywords: <code>burkholderia cenocepacia j2315</code>, this resulted in '''20 experiments''' as the results.
-*In the Filter search results drop-down menu, ''By organism'' was set to "Burkholderia cenocepacia", ''By experiment type'' was set to "RNA assay" and "Array assay", ''By array'' was kept as "All arrays"; after setting the filters, the filter button was pressed. The results now represented '''16 experiments'''; 14 out of 16 results appeared to be directly related with the J2315 strain.
+*In the Filter search results drop-down menu, ''By organism'' was set to "Burkholderia cenocepacia", ''By experiment type'' was set to "RNA assay" and "Array assay", ''By array'' was kept as "All arrays"; after setting the filters, the filter button was pressed. The results now represented '''16 experiments'''; 14 out of 16 results appeared to be directly related with the J2315 strain. It was also noticed that 12 of the 16 data-sets had the same author, ''Andrea M. Sass''.
 *Chosen Microarray dataset:
 **Accension: E-GEOD-15817
 **Data Title: Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics
 *Looking at the page for the [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15817/?query=burkholderia+cenocepacia+%22j2315%22+NOT+sass data], it was found that the related paper is titled: Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics
 ===Annotated Bibliography===
 #Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.
@@ Line 41: / Line 38: @@
 #* How many articles does this article cite: 150
 #* How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
 #Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.
 #* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946

@@ Line 30: / Line 30: @@
 ===Annotated Bibliography===
-Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.
+#Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.
-* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/18931103
+#* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/18931103
-* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/
+#* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/
-* Publisher Full Text (HTML):  http://jb.asm.org/content/191/1/261.full?sid=acd9ceae-4092-48fa-8b2e-44b6859a3653
+#* Publisher Full Text (HTML):  http://jb.asm.org/content/191/1/261.full?sid=acd9ceae-4092-48fa-8b2e-44b6859a3653
-* Publisher Full Text (PDF):  http://jb.asm.org/content/191/1/261.full.pdf+html
+#* Publisher Full Text (PDF):  http://jb.asm.org/content/191/1/261.full.pdf+html
-* Copyright: © 2009, American Society for Microbiology (information found on PDF version of article); the article and the journal is '''delayed open access''' (available 6 months after publication)
+#* Copyright: © 2009, American Society for Microbiology (information found on PDF version of article); the article and the journal is '''delayed open access''' (available 6 months after publication)
-* Publisher:  American Society for Microbiology (scientific society)
+#* Publisher:  American Society for Microbiology (scientific society)
-* Availability:  in print and online
+#* Availability:  in print and online
-* Did LMU pay a fee for this article: No
+#* Did LMU pay a fee for this article: No
-* How many articles does this article cite: 150
+#* How many articles does this article cite: 150
-* How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
+#* How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
-Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.
+#Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.
-* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946
+#* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946
-* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806911/
+#* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806911/
-* Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008724
+#* Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008724
-* Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008724&representation=PDF
+#* Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008724&representation=PDF
-* Copyright: © 2010 Yoder-Himes et al (information found on PDF version of article); the article is open-access and is distributed under a Creative Commons license.
+#* Copyright: © 2010 Yoder-Himes et al (information found on PDF version of article); the article is open-access and is distributed under a Creative Commons license.
-* Publisher: PLOS (Public Library of Science); nonprofit open-access publisher/advocate
+#* Publisher: PLOS (Public Library of Science); nonprofit open-access publisher/advocate
-* Availability: online only
+#* Availability: online only
-* Did LMU pay a fee for this article: No
+#* Did LMU pay a fee for this article: No
-* Data Found At: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15817/ ArrayExpress]
+#* Data Found At: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15817/ ArrayExpress]
-* Experiment Information: The transcriptome of a clinical and a environmental strain of ''B. cenocepacia'' was analyzed under conditions mimicking soil versus conditions mimicking the sputum resulting from cystic fibrosis. Identification and observation related to putative virulence factors was conducted. "Treatment" conditions were those mimicking CF sputum and "Control" conditions were those mimicking soil.
+#* Experiment Information: The transcriptome of a clinical and a environmental strain of ''B. cenocepacia'' was analyzed under conditions mimicking soil versus conditions mimicking the sputum resulting from cystic fibrosis. Identification and observation related to putative virulence factors was conducted. "Treatment" conditions were those mimicking CF sputum and "Control" conditions were those mimicking soil.
-* Replicate Information: Replicate experiments of the "treatment" and "control" were conducted (quadruplicates were employed using different cultures). These were biological replicates (total of 8 arrays, four biological replicates).
+#* Replicate Information: Replicate experiments of the "treatment" and "control" were conducted (quadruplicates were employed using different cultures). These were biological replicates (total of 8 arrays, four biological replicates).
-* How many articles does this article cite: 61
+#* How many articles does this article cite: 61
-* How many articles cite this article: 14
+#* How many articles cite this article: 14
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