|
|
| | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. | | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. |
| | ***All expected cross-referenced IDs were present. | | ***All expected cross-referenced IDs were present. |
| | + | ***[[File:UniProt Gene Backpage.png]] |
| | **RefSeq- NP_230721 | | **RefSeq- NP_230721 |
| | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. | | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. |
| | ***All expected cross-referenced IDs were present. | | ***All expected cross-referenced IDs were present. |
| | + | ***[[File:Refseq Gene Backpage.png]] |
| | **OrderedLocusNames- VC_0274 | | **OrderedLocusNames- VC_0274 |
| | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. | | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. |
| | ***All expected cross-referenced IDs were present. | | ***All expected cross-referenced IDs were present. |
| | + | ***[[File:Orderedlocusnames Gene Backpage.png]] |
| | **GeneID- 2612551 | | **GeneID- 2612551 |
| | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. | | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. |
| | ***All expected cross-referenced IDs were present. | | ***All expected cross-referenced IDs were present. |
| | + | ***[[File:GeneID Gene Backpage.png]] |
| | **EnsemblBacteria- AAF96503 | | **EnsemblBacteria- AAF96503 |
| | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. | | ***The Backpage for this gene included links to the following gene ID systems: UniProt, GeneOntology, OrderedLocusNames, EnsemblBacteria, EMBL, InterPro, GeneID, Pfam, and RefSeq. |
| | ***All expected cross-referenced IDs were present. | | ***All expected cross-referenced IDs were present. |
| | + | ***[[File:EnsemblBacteria Gene Backpage.png]] |
| | *Screenshot of all of the sample ID's on a MAPP: | | *Screenshot of all of the sample ID's on a MAPP: |
| | + | **[[File:All genes on MAPP.png]] |
| | | | |
| | Note: Gene IDs tested from the above gene ID systems all had complete Backpages and were successfully placed on the MAPP. | | Note: Gene IDs tested from the above gene ID systems all had complete Backpages and were successfully placed on the MAPP. |
|
|
| | | | |
| | Note: 121 errors were encountered during the creation of this new Expression Dataset. A screenshot of the error message is shown here: | | Note: 121 errors were encountered during the creation of this new Expression Dataset. A screenshot of the error message is shown here: |
| | + | *[[File:GenMAPP Errors 20151102.png]] |
| | | | |
| | ===Coloring a MAPP with expression data=== | | ===Coloring a MAPP with expression data=== |
|
|
| | * Upon entering these color sets, I saved the entire Expression Dataset by selecting Save from the Expression Dataset menu. This effectively updated my .gex file with the new Color Set. | | * Upon entering these color sets, I saved the entire Expression Dataset by selecting Save from the Expression Dataset menu. This effectively updated my .gex file with the new Color Set. |
| | | | |
| − | Screenshot: | + | Screenshot of Color Set criteria: |
| | + | *[[File:Colorset.png]] |
| | + | |
| | Note: No errors were encountered in the creation of the Color Set. | | Note: No errors were encountered in the creation of the Color Set. |
| | | | |
|
|
| | * I checked the boxes next to "Gene Ontology" and "p value", specified the results file, and then clicked "Run MAPPFinder". | | * I checked the boxes next to "Gene Ontology" and "p value", specified the results file, and then clicked "Run MAPPFinder". |
| | **This analysis took several minutes to complete. | | **This analysis took several minutes to complete. |
Exception encountered, of type "Error"
[0381459e] /biodb/fall2015/index.php?diff=next&oldid=5498&title=Bklein7_Week_9 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/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->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}