https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&feed=atom&title=Malverso_Week_8 Malverso Week 8 - Revision history 2026-06-29T21:25:42Z Revision history for this page on the wiki MediaWiki 1.25.1 https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Malverso_Week_8&diff=3436&oldid=prev Malverso: uploaded zipped folder 2015-10-27T05:10:24Z <p>uploaded zipped folder</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; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 05:10, 27 October 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="L304" >Line 304:</td> <td colspan="2" class="diff-lineno">Line 304:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*&#039;&#039;&#039;In part One of this assignment I downloaded and formatted data so that it could be interpreted by GenMAPP. This involved manipulating the data so that I could get to values that would give the information I needed in order to be able to compare gene expression between the patients samples of vibrio cholerae and the lab samples. In part Two of this assignment, we utilized both our newly created files as well as GenMAPP and MAPPFinder to be able to find out what all of the increases and decreases in the genes meant in relation to the pathogenecity of the vibrio cholerae. I specifically analyzed the genes that had significant increases in expression. Through outside resources, I was able to find that the increases in gene expression that were apparent caused an increase in protein synthesis in the vibrio cholerae found in the patients. I then found that the increase in protein signified an increase in at least one affect a human suffering from this bacterium - the diarrhea. This analysis led me to conclude that the vibrio cholerae from the patients was more dangerous and would affect humans worse than the vibrio cholerae from the lab. &#039;&#039;&#039;</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*&#039;&#039;&#039;In part One of this assignment I downloaded and formatted data so that it could be interpreted by GenMAPP. This involved manipulating the data so that I could get to values that would give the information I needed in order to be able to compare gene expression between the patients samples of vibrio cholerae and the lab samples. In part Two of this assignment, we utilized both our newly created files as well as GenMAPP and MAPPFinder to be able to find out what all of the increases and decreases in the genes meant in relation to the pathogenecity of the vibrio cholerae. I specifically analyzed the genes that had significant increases in expression. Through outside resources, I was able to find that the increases in gene expression that were apparent caused an increase in protein synthesis in the vibrio cholerae found in the patients. I then found that the increase in protein signified an increase in at least one affect a human suffering from this bacterium - the diarrhea. This analysis led me to conclude that the vibrio cholerae from the patients was more dangerous and would affect humans worse than the vibrio cholerae from the lab. &#039;&#039;&#039;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">==List of Files to Upload==</del></div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">It may be easier to zip all of these files together and then upload them as a single zipped file, rather than zipping and uploading individually (for filetypes not allowed by OpenWetware).</del></div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*Your exceptions file when you imported your data into GenMAPP: .EX.txt</del></div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; 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*I interpreted my results by looking up the definitions for any GO terms that are unfamiliar to you, which was basically all of the GO terms. I found the definitions below at http://www.geneontology.org, and categorized them based on similar definitions.
 
*I interpreted my results by looking up the definitions for any GO terms that are unfamiliar to you, which was basically all of the GO terms. I found the definitions below at http://www.geneontology.org, and categorized them based on similar definitions.
   −
*branched chain family amino acid metabolic process - The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
+
**branched chain family amino acid metabolic process - The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
−
*branched chain family amino acid biosynthetic process - The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
+
**branched chain family amino acid biosynthetic process - The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
   Exception encountered, of type "Error"
[754f34ff] /biodb/fall2015/index.php?action=history&feed=atom&title=Malverso_Week_8 Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()
Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(82): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/FeedUtils.php(155): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(325): FeedUtils::formatDiffRow()
#15 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(290): HistoryAction->feedItem()
#16 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(130): HistoryAction->feed()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/FormlessAction.php(43): HistoryAction->onView()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): FormlessAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}