BIOL367/F10:GenMAPP and MAPPFinder Protocols - Revision history

Jennifer Okonta: /* MAPPFinder Procedure */ uniprot edit

Jennifer Okonta — Thu, 28 Oct 2010 18:08:19 GMT

MAPPFinder Procedure: uniprot edit

←Older revision		Revision as of 18:08, 28 October 2010
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	** '''Compare your list with your buddy who used a different version of the Gene Database. Are your terms the same or different? Why do you think that is? Record your answer in your individual journal entry.'''		** '''Compare your list with your buddy who used a different version of the Gene Database. Are your terms the same or different? Why do you think that is? Record your answer in your individual journal entry.'''
	* One of the things you can do in MAPPFinder is to find the Gene Ontology term(s) with which a particular gene is associated. First, in the main MAPPFinder Browser window, click on the button "Collapse the Tree". Then, you can search for the genes that were mentioned by Merrell et al. (2002), VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583. Type the identifier for one of these genes into the MAPPFinder browser gene ID search field. The GO term(s) that are associated with that gene will be highlighted in blue. '''List the GO terms associated with each of those genes in your individual journal. (Note: they might not all be found.) Are they the same as your buddy who is using a different Gene Database? Why or why not?'''		* One of the things you can do in MAPPFinder is to find the Gene Ontology term(s) with which a particular gene is associated. First, in the main MAPPFinder Browser window, click on the button "Collapse the Tree". Then, you can search for the genes that were mentioned by Merrell et al. (2002), VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583. Type the identifier for one of these genes into the MAPPFinder browser gene ID search field. The GO term(s) that are associated with that gene will be highlighted in blue. '''List the GO terms associated with each of those genes in your individual journal. (Note: they might not all be found.) Are they the same as your buddy who is using a different Gene Database? Why or why not?'''
-	* Click on one of the GO terms that are associated with one of the genes you looked up in the previous step. A MAPP will open listing all of the genes (as boxes) associated with that GO term. Moreover, the genes on the MAPP will be color-coded with the gene expression data from the microarray experiment. '''List in your journal entry the name of the GO term you clicked on and whether the expression of the gene you were looking for changed significantly in the experiment.'''	+	* Click on one of the GO terms that are associated with one of the genes you looked up in the previous step. A MAPP will open listing all of the genes (as boxes) associated with that GO term. The genes named within the map are based on the UniProt identification system. To match the gene of interest to its identification go to the [http://www.uniprot.org/ UniProt site] and type in your gene ID into the search bar. Moreover, the genes on the MAPP will be color-coded with the gene expression data from the microarray experiment. '''List in your journal entry the name of the GO term you clicked on and whether the expression of the gene you were looking for changed significantly in the experiment.'''
	** Double-click on the gene box. This will open a Internet Explorer window called the "Backpage" for this gene. This page has links to pages for this gene in the public databases. '''Click on the links to find out the function of this gene and record your answer in your individual journal page.'''		** Double-click on the gene box. This will open a Internet Explorer window called the "Backpage" for this gene. This page has links to pages for this gene in the public databases. '''Click on the links to find out the function of this gene and record your answer in your individual journal page.'''
	** The MAPP that has just been created is stored in the directory, C:\GenMAPP 2 Data\MAPPs\VC GO. '''Upload this file and link to it in your journal.'''		** The MAPP that has just been created is stored in the directory, C:\GenMAPP 2 Data\MAPPs\VC GO. '''Upload this file and link to it in your journal.'''

Kam D. Dahlquist: added category to page

Kam D. Dahlquist — Tue, 26 Oct 2010 16:01:53 GMT

added category to page

←Older revision		Revision as of 16:01, 26 October 2010
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	# The MAPP you looked at: <code>.mapp</code>		# The MAPP you looked at: <code>.mapp</code>
	# The MAPPFinder GO mappings file: <code>.gmf</code>		# The MAPPFinder GO mappings file: <code>.gmf</code>
		+
		+	[[Category:BIOL367/F10]]

Kam D. Dahlquist: /* Map Onto Biological Pathways (GenMAPP & MAPPFinder) */ link to new Vc gdb

Kam D. Dahlquist — Tue, 26 Oct 2010 03:45:54 GMT

Map Onto Biological Pathways (GenMAPP & MAPPFinder): link to new Vc gdb

←Older revision		Revision as of 03:45, 26 October 2010
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	* For the exercise today, you will need to download the appropriate ''Vibrio cholerae'' Gene Database.		* For the exercise today, you will need to download the appropriate ''Vibrio cholerae'' Gene Database.
	** Half of the class will use the Vc-Std_External_20090622.gdb Gene Database that was created by the Fall 2008 Biological Databases class.		** Half of the class will use the Vc-Std_External_20090622.gdb Gene Database that was created by the Fall 2008 Biological Databases class.
-	*** To download this Gene Database, [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020090622/Vc-Std_External_20090622.zip/download follow this link to the XMLPipeDB SourceForge Download page].	+	*** To download this Gene Database, [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020090622/Vc-Std_External_20090622.zip/download follow '''''this link''''' to the XMLPipeDB SourceForge Download page].
	** Half of the class will use a new Vc-Std_External_20101022.gdb Gene Database that was created by Drs. Dahlquist and Dionisio this weekend.		** Half of the class will use a new Vc-Std_External_20101022.gdb Gene Database that was created by Drs. Dahlquist and Dionisio this weekend.
		+	*** To download this Gene Database, [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download follow '''''this link''''' to the XMLPipeDB SourceForge Download page].
	** The members of a pair should each choose a different gene database.		** The members of a pair should each choose a different gene database.
	* Click on the link for the Gene Database to which you have been assigned, download the file, and save it into the folder C:\GenMAPP 2 Data\Gene Databases, and extract it.		* Click on the link for the Gene Database to which you have been assigned, download the file, and save it into the folder C:\GenMAPP 2 Data\Gene Databases, and extract it.

Kam D. Dahlquist: /* GenMAPP Expression Dataset Manager Procedure */ note to upload exceptions file

Kam D. Dahlquist — Tue, 26 Oct 2010 00:46:49 GMT

GenMAPP Expression Dataset Manager Procedure: note to upload exceptions file

←Older revision		Revision as of 00:46, 26 October 2010
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	*** '''Record the number of errors. For your journal assignment, open the .EX.txt file and use the Data > Filter > Autofilter function to determine what the errors were for the rows that were not converted. Record this information in your individual journal page.'''		*** '''Record the number of errors. For your journal assignment, open the .EX.txt file and use the Data > Filter > Autofilter function to determine what the errors were for the rows that were not converted. Record this information in your individual journal page.'''
	*** '''It is likely that you will have a different number of errors than your buddy who is using a different version of the ''Vibrio cholerae'' Gene Database. Which of you has more errors? Why do you think that is? Record your answers in your journal page.'''		*** '''It is likely that you will have a different number of errors than your buddy who is using a different version of the ''Vibrio cholerae'' Gene Database. Which of you has more errors? Why do you think that is? Record your answers in your journal page.'''
		+	*** '''Upload your exceptions file: <code>EX.txt</code> to your wiki page.
	* Customize the new Expression Dataset by creating new Color Sets which contain the instructions to GenMAPP for displaying data on MAPPs.		* Customize the new Expression Dataset by creating new Color Sets which contain the instructions to GenMAPP for displaying data on MAPPs.
	** Color Sets contain the instructions to GenMAPP for displaying data from an Expression Dataset on MAPPs. Create a Color Set by filling in the following different fields in the Color Set area of the Expression Dataset Manager: a name for the Color Set, the gene value, and the criteria that determine how a gene object is colored on the MAPP. Enter a name in the Color Set Name field that is 20 characters or fewer.		** Color Sets contain the instructions to GenMAPP for displaying data from an Expression Dataset on MAPPs. Create a Color Set by filling in the following different fields in the Color Set area of the Expression Dataset Manager: a name for the Color Set, the gene value, and the criteria that determine how a gene object is colored on the MAPP. Enter a name in the Color Set Name field that is 20 characters or fewer.

Kam D. Dahlquist: /* List of Files to Upload */ made list with extensions

Kam D. Dahlquist — Tue, 26 Oct 2010 00:45:38 GMT

List of Files to Upload: made list with extensions

←Older revision		Revision as of 00:45, 26 October 2010
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	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).		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).
		+
		+	# Your exceptions file when you imported your data into GenMAPP: <code>.EX.txt</code>
		+	# Your Expression Dataset file: <code>.gex</code>
		+	# Your GO results file: <code>XXX-CriterionX-GO.txt</code>
		+	# Your GO results saved as an Excel spreadsheet with filters applied: <code>.xls</code>
		+	# The MAPP you looked at: <code>.mapp</code>
		+	# The MAPPFinder GO mappings file: <code>.gmf</code>

Kam D. Dahlquist: /* MAPPFinder Procedure */ started section for list to upload

Kam D. Dahlquist — Tue, 26 Oct 2010 00:41:27 GMT

MAPPFinder Procedure: started section for list to upload

←Older revision		Revision as of 00:41, 26 October 2010
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	* '''Interpret your results. Look up the definitions for any GO terms that are unfamiliar to you. The "official" definitions for GO terms can be found at [http://www.geneontology.org http://www.geneontology.org]. You can use one of the online biological dictionaries as a supplement, if needed. Write a paragraph relating the results of this GO analysis to the experiment performed (comparing laboratory-grown and patient-derived ''Vibrio cholerae''. You need to give a biological interpretation of what do each of these GO terms in your filtered list have to to with the pathogenecity of the bacterium? You may consult with your partner on this, but your explanation on your individual journal page needs to be in your own words. This is where the real "brain power" comes in with interpreting DNA microarray data. Even experienced scientists struggle with this part. Use your creativity as a scientist to stretch your brain in this question.'''		* '''Interpret your results. Look up the definitions for any GO terms that are unfamiliar to you. The "official" definitions for GO terms can be found at [http://www.geneontology.org http://www.geneontology.org]. You can use one of the online biological dictionaries as a supplement, if needed. Write a paragraph relating the results of this GO analysis to the experiment performed (comparing laboratory-grown and patient-derived ''Vibrio cholerae''. You need to give a biological interpretation of what do each of these GO terms in your filtered list have to to with the pathogenecity of the bacterium? You may consult with your partner on this, but your explanation on your individual journal page needs to be in your own words. This is where the real "brain power" comes in with interpreting DNA microarray data. Even experienced scientists struggle with this part. Use your creativity as a scientist to stretch your brain in this question.'''
	* '''There is one other file you need to save to your journal page. It has a .gmf extension and should be in the same fold as the .gex file that you created with the GenMAPP Expression Dataset Manager. You will need this file to re-open your results in MAPPFinder.'''		* '''There is one other file you need to save to your journal page. It has a .gmf extension and should be in the same fold as the .gex file that you created with the GenMAPP Expression Dataset Manager. You will need this file to re-open your results in MAPPFinder.'''
		+
		+	==== List of Files to Upload ====
		+
		+	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).

Kam D. Dahlquist: /* MAPPFinder Procedure */ clarified uploading of files

Kam D. Dahlquist — Tue, 26 Oct 2010 00:40:04 GMT

MAPPFinder Procedure: clarified uploading of files

←Older revision		Revision as of 00:40, 26 October 2010
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	** "XXX" refers to the name you gave to your results file.		** "XXX" refers to the name you gave to your results file.
	** "CriterionX" refers to either "Criterion0" or "Criterion1". Since computers start counting at zero, "Criterion0" is the first criterion in the list you clicked on ("Increased" if you followed the directions) and "Criterion1" is the second criterion in the list you clicked on ("Decreased" if you followed the directions).		** "CriterionX" refers to either "Criterion0" or "Criterion1". Since computers start counting at zero, "Criterion0" is the first criterion in the list you clicked on ("Increased" if you followed the directions) and "Criterion1" is the second criterion in the list you clicked on ("Decreased" if you followed the directions).
-	** '''Upload ~~both of~~ your results ~~files~~ to your journal page.'''	+	** '''Upload your results file to your journal page.'''
	* Launch Microsoft Excel. Open the copies of the .txt files in Excel (you will need to "Show all files" and click "Finish" to the wizard that will open your file). This will show you the same data that you saw in the MAPPFinder Browser, but in tabular form.		* Launch Microsoft Excel. Open the copies of the .txt files in Excel (you will need to "Show all files" and click "Finish" to the wizard that will open your file). This will show you the same data that you saw in the MAPPFinder Browser, but in tabular form.
	* Look at the top of the spreadsheet. There are rows of information that give you the background information on how MAPPFinder made the calculations. '''Compare this information with your buddy who used a different version of the Vibrio Gene Database. Which numbers are different? Why are they different? Record this information in your individual journal entry.'''		* Look at the top of the spreadsheet. There are rows of information that give you the background information on how MAPPFinder made the calculations. '''Compare this information with your buddy who used a different version of the Vibrio Gene Database. Which numbers are different? Why are they different? Record this information in your individual journal entry.'''
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	* '''Interpret your results. Look up the definitions for any GO terms that are unfamiliar to you. The "official" definitions for GO terms can be found at [http://www.geneontology.org http://www.geneontology.org]. You can use one of the online biological dictionaries as a supplement, if needed. Write a paragraph relating the results of this GO analysis to the experiment performed (comparing laboratory-grown and patient-derived ''Vibrio cholerae''. You need to give a biological interpretation of what do each of these GO terms in your filtered list have to to with the pathogenecity of the bacterium? You may consult with your partner on this, but your explanation on your individual journal page needs to be in your own words. This is where the real "brain power" comes in with interpreting DNA microarray data. Even experienced scientists struggle with this part. Use your creativity as a scientist to stretch your brain in this question.'''		* '''Interpret your results. Look up the definitions for any GO terms that are unfamiliar to you. The "official" definitions for GO terms can be found at [http://www.geneontology.org http://www.geneontology.org]. You can use one of the online biological dictionaries as a supplement, if needed. Write a paragraph relating the results of this GO analysis to the experiment performed (comparing laboratory-grown and patient-derived ''Vibrio cholerae''. You need to give a biological interpretation of what do each of these GO terms in your filtered list have to to with the pathogenecity of the bacterium? You may consult with your partner on this, but your explanation on your individual journal page needs to be in your own words. This is where the real "brain power" comes in with interpreting DNA microarray data. Even experienced scientists struggle with this part. Use your creativity as a scientist to stretch your brain in this question.'''
	* '''There is one other file you need to save to your journal page. It has a .gmf extension and should be in the same fold as the .gex file that you created with the GenMAPP Expression Dataset Manager. You will need this file to re-open your results in MAPPFinder.'''		* '''There is one other file you need to save to your journal page. It has a .gmf extension and should be in the same fold as the .gex file that you created with the GenMAPP Expression Dataset Manager. You will need this file to re-open your results in MAPPFinder.'''
-	**''Yes, there were a lot of different files to keep track of in this assignment. :)''

Kam D. Dahlquist: /* MAPPFinder Procedure */

Kam D. Dahlquist — Tue, 26 Oct 2010 00:29:29 GMT

MAPPFinder Procedure

←Older revision		Revision as of 00:29, 26 October 2010
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	* Click on "Find File" and choose the your Expression Dataset file, for example, "MyDataset.gex", and click OK.		* Click on "Find File" and choose the your Expression Dataset file, for example, "MyDataset.gex", and click OK.
	** MAPPFinder may have found it for you already if you already had it open in GenMAPP, in which case, you just need to click OK.		** MAPPFinder may have found it for you already if you already had it open in GenMAPP, in which case, you just need to click OK.
-	* Choose the Color Set and Criteria with which to filter the data. ~~Control-click~~ on ~~both~~ the "Increased" and "Decreased" criteria in the right-hand box.	+	* Choose the Color Set and Criteria with which to filter the data. Click on either the "Increased" and "Decreased" criteria in the right-hand box, depending on which one your group is doing. (You could select both by holding down the Control key while clicking).
	* Check the boxes next to "Gene Ontology" and "p value".		* Check the boxes next to "Gene Ontology" and "p value".
	* Click the "Browse" button and create a meaningful filename for your results.		* Click the "Browse" button and create a meaningful filename for your results.

Kam D. Dahlquist: /* MAPPFinder Procedure */ link to group list

Kam D. Dahlquist — Tue, 26 Oct 2010 00:05:24 GMT

MAPPFinder Procedure: link to group list

←Older revision		Revision as of 00:05, 26 October 2010
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	=== MAPPFinder Procedure ===		=== MAPPFinder Procedure ===

-	'''''Note: You and your buddy will both do the same criterion, either "Increased" or "Decreased", but your group does not need to do both "Increased" and "Decreased" Sign up for the criterion you want on the Group list so that we can make sure that as a class we are covering both criteria.'''''	+	'''''Note: You and your buddy will both do the same criterion, either "Increased" or "Decreased", but your group does not need to do both "Increased" and "Decreased" Sign up for the criterion you want on the [[BIOL367/F10#Groups_3 \| Group list]] so that we can make sure that as a class we are covering both criteria.'''''

	* Launch the MAPPFinder program (or from within GenMAPP, select Tools > MAPPFinder.		* Launch the MAPPFinder program (or from within GenMAPP, select Tools > MAPPFinder.

Kam D. Dahlquist: /* MAPPFinder Procedure */ said only have to do increased OR decreased

Kam D. Dahlquist — Tue, 26 Oct 2010 00:04:36 GMT

MAPPFinder Procedure: said only have to do increased OR decreased

←Older revision		Revision as of 00:04, 26 October 2010
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	=== MAPPFinder Procedure ===		=== MAPPFinder Procedure ===

-	'''''Note: You will need to ~~complete the journal assignment for~~ both ~~the~~ "Increased" and "Decreased" criteria.'''''	+	'''''Note: You and your buddy will both do the same criterion, either "Increased" or "Decreased", but your group does not need to do both "Increased" and "Decreased" Sign up for the criterion you want on the Group list so that we can make sure that as a class we are covering both criteria.'''''

	* Launch the MAPPFinder program (or from within GenMAPP, select Tools > MAPPFinder.		* Launch the MAPPFinder program (or from within GenMAPP, select Tools > MAPPFinder.