https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Ksherbina_Week_10Ksherbina Week 10 - Revision history2026-04-30T04:22:31ZRevision history for this page on the wikiMediaWiki 1.20.3https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Week_10&diff=4765&oldid=prevKsherbina: /* Locating journal articles published on microarray datasets not in EBI ArrayExpress */ Added steps to look up microarray articles in the Web of Science2013-11-01T04:59:28Z<p><span dir="auto"><span class="autocomment">Locating journal articles published on microarray datasets not in EBI ArrayExpress: </span> Added steps to look up microarray articles in the Web of Science</span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 04:59, 1 November 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 50:</td>
<td colspan="2" class="diff-lineno">Line 50:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*'''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.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*'''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.'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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|Locate journal article describing C. trachomatis reference genome]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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|Locate journal article describing C. trachomatis reference genome]].</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#In the citation for the article, click on the link for the number of times that article was cited by other articles.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#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.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*'''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.'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- QUESTION FOR DR. DAHLQUIST: Are we only looking at articles that collected data using microarrays created from the species genome (some articles used human arrays)?--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- QUESTION FOR DR. DAHLQUIST: Are we only looking at articles that collected data using microarrays created from the species genome (some articles used human arrays)?--></div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Week_10&diff=4763&oldid=prevKsherbina: /* Locating journal articles published on microarray datasets not in EBI ArrayExpress */ Added another step2013-11-01T04:52:18Z<p><span dir="auto"><span class="autocomment">Locating journal articles published on microarray datasets not in EBI ArrayExpress: </span> Added another step</span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 04:52, 1 November 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 49:</td>
<td colspan="2" class="diff-lineno">Line 49:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Click on the "Search" button to search for articles meeting the filter criteria.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Click on the "Search" button to search for articles meeting the filter criteria.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*'''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.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*'''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.'''</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#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|Locate journal article describing C. trachomatis reference genome]].</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- QUESTION FOR DR. DAHLQUIST: Are we only looking at articles that collected data using microarrays created from the species genome (some articles used human arrays)?--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- QUESTION FOR DR. DAHLQUIST: Are we only looking at articles that collected data using microarrays created from the species genome (some articles used human arrays)?--></div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Week_10&diff=4757&oldid=prevKsherbina: /* Locate journal article describing C. trachomatis reference genome */ Looked up how to search for the reference genome article on Web of Science.2013-11-01T04:31:25Z<p><span dir="auto"><span class="autocomment">Locate journal article describing C. trachomatis reference genome: </span> Looked up how to search for the reference genome article on Web of Science.</span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 04:31, 1 November 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 12:</td>
<td colspan="2" class="diff-lineno">Line 12:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Click on the "Search" button to search for an article satisfying the filters that were set.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#*Click on the "Search" button to search for an article satisfying the filters that were set.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*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.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Go to the Web of Science database through the link provided in the [http://libguides.lmu.edu/BIOL367 LibGuide] for the class.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#In the first blank search field, type in part of the title of the article about the reference genome.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*For the article aforementioned, I typed in "obligate intracellular pathogen".</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#In the drop down menu to the right, select "Title".</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#In the next blank search field, type in the author's name.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*For the article aforementioned, I typed in "Stephens".</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Click on the "Search" button. One of the results should be the article that you found on the reference genome.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#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.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Locate journal articles that measure gene expression==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Locate journal articles that measure gene expression==</div></td></tr>
</table>Ksherbinahttps://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Ksherbina_Week_10&diff=4721&oldid=prevKsherbina: /* Locate journal articles that measure gene expression */ Made sections2013-11-01T03:41:23Z<p><span dir="auto"><span class="autocomment">Locate journal articles that measure gene expression: </span> Made sections</span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 03:41, 1 November 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 16:</td>
<td colspan="2" class="diff-lineno">Line 16:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Locate journal articles that measure gene expression==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Locate journal articles that measure gene expression==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Locating microarray data on EBI ArrayExpress===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Go to the [http://www.ebi.ac.uk/arrayexpress/ EBI ArrayExpress] database.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Go to the [http://www.ebi.ac.uk/arrayexpress/ EBI ArrayExpress] database.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Click on "Experiments" in the navigation toolbar toward the top of the website.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Click on "Experiments" in the navigation toolbar toward the top of the website.</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 29:</td>
<td colspan="2" class="diff-lineno">Line 30:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#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.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Locating journal articles published on microarray datasets not in EBI ArrayExpress===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Go to the PubMed site through the link provided in the [http://libguides.lmu.edu/BIOL367 LibGuide] for the class.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Go to the PubMed site through the link provided in the [http://libguides.lmu.edu/BIOL367 LibGuide] for the class.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Beneath the search bar at the top of the page, click on the "Advanced" link.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#Beneath the search bar at the top of the page, click on the "Advanced" link.</div></td></tr>
</table>Ksherbina
#Go to the "By organism" drop down menu in the "Filter Experiments" section. Select the species ''Chlamydia trachomatis''.
#Go to the "By organism" drop down menu in the "Filter Experiments" section. Select the species ''Chlamydia trachomatis''.
#Click on the "Filter" button to locate the microarray datasets on the database for the selected species.
#Click on the "Filter" button to locate the microarray datasets on the database for the selected species.