Blitvak Week 9 - Revision history

Blitvak: mentioned that the top GO terms for the 2010 database came from my week 8 partner, Anu

2015-11-04T04:34:08Z

mentioned that the top GO terms for the 2010 database came from my week 8 partner, Anu

Blitvak: added a few details about how the new database functioned with GenMAPP

2015-11-03T22:44:58Z

added a few details about how the new database functioned with GenMAPP

Blitvak: slightly fleshed out the "hypotheses"

2015-11-03T07:41:09Z

slightly fleshed out the "hypotheses"

Blitvak: added link to the excel workbook that was used in the MATCH analysis

2015-11-03T07:34:48Z

added link to the excel workbook that was used in the MATCH analysis

@@ Line 218: / Line 218: @@
 Note: The top GO terms appear very similar to those found using the 2010 database with the same settings. MAPPFinder was successfully launched and everything appeared to be in order.
-*As its top GO terms, the 2010 Database had:
+*As its top GO terms, my partner for the week 8 assignment (Anu V.) found that the 2010 Database had:
 **#branched chain family amino acid metabolic process
 **#branched chain family amino acid biosynthetic process

@@ Line 183: / Line 183: @@
 **VC0122 was also found and all of the cross-referenced IDs are present (according to the GO terms, this gene seems to be related to ''cAMP biosynthetic process'' and ''adenylate cyclase activity'')
-Note: All cross-referenced IDs were present for both of these sample Gene IDs
+Note: All cross-referenced IDs were present for both of these sample Gene IDs. No crashing or issues at this step.
 ===Creating an Expression Dataset in the Expression Dataset Manager===
@@ Line 191: / Line 191: @@
 **None of these IDs were present in the UniProt XML (had no chance of being imported, since they weren't even present in the files employed for the export of the database)
-Note: The number of errors for this database (121) is the same as the number of errors for the 2010 database
+Note: The number of errors for this database (121) is the same as the number of errors for the 2010 database. A dataset was successfully created using the new database.
 ===Coloring a MAPP with expression data===
@@ Line 201: / Line 201: @@
 **Both criteria were added and the whole Expression Dataset was saved and the Expression Dataset Manager was exited
-Note: No issues with creating the color-sets
+Note: No issues with creating the color-sets. The increased and decreased criteria were successfully defined.
 ===Running MAPPFinder===
@@ Line 216: / Line 216: @@
 *[[File:TOP_GO_terms_BL_week_9.png]]
-Note: The top GO terms appear very similar to those found using the 2010 database with the same settings.
+Note: The top GO terms appear very similar to those found using the 2010 database with the same settings. MAPPFinder was successfully launched and everything appeared to be in order.
 *As its top GO terms, the 2010 Database had:
@@ Line 230: / Line 230: @@
 **#cellular nitrogen compound biosynthetic process
-*Note: It appears that both sets of top GO terms heavily involve the metabolic pathways/processes related to amino acids, nitrogenous bases, and nucleosides (with respect to the Increased expression criterion). In this way, it appears that the 2015 database is fairly similar to the 2010 database (seems to cover as many genes, with similar information)
+*Final Notes: It appears that both sets of top GO terms heavily involve the metabolic pathways/processes related to amino acids, nitrogenous bases, and nucleosides (with respect to the Increased expression criterion). In this way, it appears that the 2015 database is fairly similar to the 2010 database (seems to cover as many genes, with similar information). The new database seemed to function smoothly with GenMAPP; no crashes, issues, or hang-ups were found while using this database.
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@@ Line 104: / Line 104: @@
 **[[File:BL MATCHUTILITY WEEK9.png]]
 Are your results the same as you got for the TallyEngine?  Why or why not?
-*These results are not the same as what was found using TallyEngine (3831 results were found through TallyEngine). It is suspected that the match command pattern is not fully representative of everything that falls under ''OrderedLocusNames'' (the fault, it is believed, lies with match and not with TallyEngine)
+*These results are not the same as what was found using TallyEngine (3831 results were found through TallyEngine). It is suspected that the match command pattern is not fully representative of everything that falls under ''OrderedLocusNames'' (the fault, it is believed, lies with match and not with TallyEngine); it seems that some IDs are being missed by match
 ===Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
@@ Line 110: / Line 110: @@
 *It was realized that the ''gene/name'' tags in the XML file end up in the ''genenametype'' table (source: [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways |the wiki page regarding database quality analysis]]
 *In ''pgAdmin III'', the query <code>select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_[0-9][0-9][0-9][0-9]';</code> was issued via the SQL Query menu in order to further validate the PostgreSQL Database Results according to TallyEngine
-*2737 unique matches were found in ''pgAdmin III'' (postgres database results). These results are not the same as what was found by TallyEngine and are slightly different from what was found using XMLPipeDB match (1 off). It seems that the results are really close to what the Match utility found because it utilizes the same pattern ('VC_[0-9][0-9][0-9][0-9]')
+*2737 unique matches were found in ''pgAdmin III'' (postgres database results). These results are not the same as what was found by TallyEngine and are slightly different from what was found using XMLPipeDB match (1 off). It seems that the results are really close to what the Match utility found because it utilizes the same pattern ('VC_[0-9][0-9][0-9][0-9]'). It is also possible that the entries in the postgresSQL table are slightly different from those in other sources (which could explain the 1 off value, compared to what match found); it is predicted that both the match query and the SQL query are not taking into account the same set of IDs
 **[[File:BL PSQL COUNT WEEK9.png]]

@@ Line 155: / Line 155: @@
   '''MATCH:3 to 1''' : <code>=MATCH(C2, A$2:A$3833,0)</code>
   '''MATCH:3 to 2''' : <code>=MATCH(C2, B$2:B$3832,0)</code>
 ====MATCH results analysis====
 *''ctrl+F'' was utilized in order to find instances of '''#N/A''' among all of the MATCH columns (some options included, Look In: ''Values'', Find What: ''#N/A'', Find All); eight cases of '''#N/A''' were found
@@ Line 160: / Line 161: @@
 *The last two cases of '''#N/A''' were found to be the result of the presence of '''VC_A0360.1''' in position '''3093''' within the ''IDs FROM 'ORDEREDLOCUSNAMES (1)'' column, and in position '''3092''' within the ''IDs FROM postgreSQL (3)'' column
 *It seems apparent that there exist some entries in the 'ORDEREDLOCUSNAMES' that are not accounted for by the MATCH utility ('''VC_A0360.1'''); it is also clear that there are two entries acting as one entry within the postgreSQL output ('''VC_1738/VC_1739'''). '''VC_A0360.1''' also exists within the postgreSQL output.
 ===Further Quality Assurance Work===
 *Using the Match utility, <code>java -jar xmlpipedb-match-1.1.1.jar "VC_A?[0-9][0-9][0-9][0-9](.1)?" < uniprot-organism%3A243277.xml</code> was inputted into the Windows command line in order to get all 3832 possible unique matches (includes '''VC_A0360.1''')
@@ Line 228: / Line 230: @@
 **#cellular nitrogen compound biosynthetic process
-*It appears that both sets of top GO terms heavily involve the metabolic pathways/processes related to amino acids, nitrogenous bases, and nucleosides (with respect to the Increased expression criterion). In this way, it appears that the 2015 database is fairly similar to the 2010 database (seems to cover as many genes, with similar information)
+*Note: It appears that both sets of top GO terms heavily involve the metabolic pathways/processes related to amino acids, nitrogenous bases, and nucleosides (with respect to the Increased expression criterion). In this way, it appears that the 2015 database is fairly similar to the 2010 database (seems to cover as many genes, with similar information)
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