Troque Week 9

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Export Information

Version of GenMAPP Builder:

  • gmbuilder-3.0.0-build-5

Computer on which export was run:

  • The right-most computer at the very back of the room when facing the wide whiteboard/the computer at the back row that is closest to the door.

Postgres Database name:

  • V_cholerae_20151027_gmb-5_TR

UniProt XML filename (give filename and upload and link to compressed file):

GO OBO-XML filename (give filename and upload and link to compressed file):

GOA filename (give filename and upload and link to compressed file):

Name of .gdb file (give filename and upload and link to compressed file):

  • Time taken to export: 5 hours, 33 minutes and 40 seconds
    • Start time: 3:52:13 PM PDT
    • End time: 9:25:53 PM PDT
    • Note: I was out of town (went to D.C./Maryland for a research conference) so I couldn't check when the export finished, but it was a good thing that I logged in as myself (instead of the general student account) on the computer since it preserved the windows I had open from before I was left.

TallyEngine

  • Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
    • Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
    • Choose the UniProt and GO OBO XML files that was uploaded from the previous sections of this assignment.
    • Here is the screenshot of the tally result:

Tally results TR 20151102.jpg

Using XMLPipeDB match to Validate the XML Results from the TallyEngine

Follow the instructions found on this page to run XMLPipeDB match.

  • Note: When I tried downloading the jar file, it wasn't in the zip file that I downloaded when I clicked the link provided in the protocol. However, thanks to Kevin Wyllie who gave me the file, I managed to acquire it.
  • Note: I created my own directory (called TrixRoq) in order to store all the files I downloaded into one single folder to differentiate it from the rest of the files in the ThawSpace disk. I also made a directory (called Working Data) in the ThawSpace0 disk in order to separate the source data from the data I worked with (per class suggestions from Dr. Dahlquist).
  • As a result, I had to cd to these directories first before using the command for using Match.
    • In order to change into the ThawSpace0\TrixRoq\Working Data directory, use the following commands on the command prompt window:
T: && cd "TrixRoq\Working Data"
  • The command I used once inside the directory I want is:
java -jar xmlpipedb-match-1.1.1.jar "VC_[0-9][0-9][0-9][0-9]" < uniprot-organism%3A243277.xml"
  • The results are as follows:

Command prompt results TR 20151102.jpg

These results did not match up with what the TallyEngine gave (TallyEngine: 3831 vs. Match: 2738)

  • As a result, the commands would have to be modified somehow so that the numbers match. Since the original command only accounted for the pattern with VC_####, we also have to account for the pattern for VC_A?####. The new command is as follows:
   java -jar xmlpipedb-match-1.1.1.jar "VC_A?[0-9][0-9][0-9][0-9]" < uniprot-organism%3A243277.xml > command_prompt_results_TR.txt

which gave the results:

Command prompt results updated TR 20151102.jpg

and saved it to the file "command_prompt_results_TR.txt"

Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine

For more information, see this page.

You can also look for counts at the SQL level, using some variation of a select count(*) query. This requires some knowledge of which table received what data. Here’s an initial tip: the gene/name tags in the XML file land in the genenametype table. A query on this table counting values from this table that were marked as ordered locus in the XML file matching the pattern VC_[0-9][0-9][0-9][0-9] would look like this: 

select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_[0-9][0-9][0-9][0-9]';

In pgAdmin III, you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the SQL Editor tab, then clicking on the green triangular Play button to run.

Pgadminiii-query.png

Are your results the same as reported by the TallyEngine? Why or why not?

OriginalRowCounts Comparison

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file:

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

Note:

Visual Inspection

Perform visual inspection of individual tables to see if there are any problems.

  • Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
  • Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

.gdb Use in GenMAPP

Note:

Putting a gene on the MAPP using the GeneFinder window

  • Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

Creating an Expression Dataset in the Expression Dataset Manager

  • How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

Coloring a MAPP with expression data

Note:

Running MAPPFinder

Note:

Assignment Links

Weekly Assignments

Individual Journal Entries

Shared Journal Entries

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