Zrusso Week 9
From OpenWetWare
GenMAPP and MAPPFinder Usage in Week 9
Number of errors detected
- I detected 772 errors out of 5221 records in the old database from 2009
- Richard detected 121 errors out of 5221 records while using the new database from 2010
- I have more errors, which is to be expected from an older database that is not as comprehensive as the newer database which includes data from more sources.
Top 10 Gene Ontology Terms from MAPPFinder
- For me
- Localization
- Cellular Biopolymer Biosynthetic Process
- Biopolymer Biosynthetic Process
- Cellular Macromolecule Biosynthetic Process
- Macromolecule Biosynthetic Process
- Cellular Macromolecule Metabolic Process
- Macromolecule Metabolic Process
- Cell Projection Organization
- Biopolymer Metabolic Process
- Transporter Activity
- For Richard
- Branched Chain Family Amino Acid Metabolic Process
- Branched Chain Family Amino Acid Biosynthetic Process
- IMP Biosynthetic Process
- IMP Metabolic Process
- Arginine Metabolic Process
- Cellular Nitrogen Compound Biosynthetic Process
- Leucine Biosynthetic Process
- Leucine Metabolic Process
- Amine Biosynthetic Process
- Arginine Biosynthetic Process
Genes Listed in Merrell et al. (2003
- For Me
- VC0028 - NOT FOUND
- VC0941 - NOT FOUND
- VC0869 - NOT FOUND
- VC0051 - NOT FOUND
- VC0647
- mRNA catabolic process
- RNA processing
- cytoplasm
- RNA binding
- 3'-5' exoribonuclease activity
- transferase activity
- nucleotidyltransferase activity
- polyribonucleotide nucleotidyltransferase activity
- VC0468 - NOT FOUND
- VC2350 - NOT FOUND
- VCA0583
- transport
- outer membrane-bounded periplasmic space
- transporter activity
- For Richard
- VC0028
- metal ion binding
- iron-sulfur cluster binding
- 4 iron, 4 sulfur cluster binding
- catalytic activity
- lyase activity
- dihydroxy-acid dehydratase
- VC0941
- pyridoxal phosphate binding
- catalytic activity
- glycine hydroxymethyltransferase
- VC0869
- nucleotide binding
- ATP binding
- catalytic activity
- ligase activity
- phosphoribosilformylglycinamidine synthase activity
- VC0051
- nucleotide binding
- ATP binding
- catalytic activity
- lyase activity
- carboxy-lyase activity
- phosphoribosylaminoimidazole caroxylase activity
- VC0647
- nucleotidyltransferase activity
- polyribonucleotide nucleotidyltransferase activity
- VC0468
- metal ion binding
- nucleotide binding
- ATP binding
- catalytic activity
- ligase activity
- glutathione synthase activity
- VC2350
- catalytic activity
- lyase activity
- deoxyribose-phosphate aldolase activity
- VCA0583
- outer membrane-bounded periplasmic space
- VC0028
- For Me
VCA0583
- I picked VCA0583 as the gene to examine more closely
- Its acession number ID is Q9KM06
- After reading the UniProt and Pfam and Gene Ontology websites on this gene, it was clear that all knew that VCA0583 was part of the transport activity in the cell membrane, but none were very clear on what it did exactly. the closest was Pfam which thought it wasn't actually a transporter, merely a binding site for a signalling molecule which precluded a transport of some type.
Data from txt file
- From Me
- 339 probes met the [Avg_LogFC_all] > .25 AND [Pvalue] < .05 criteria.
- 291 probes meeting the filter linked to a UniProt ID.
- 184 genes meeting the criterion linked to a GO term.
- 5221 Probes in this dataset
- 4449 Probes linked to a UniProt ID.
- 1990 Genes linked to a GO term.
- The z score is based on an N of 1990 and a R of 184 distinct genes in the GO.
- From Richard
- 339 probes met the [Avg_LogFC_all] > .25 AND [Pvalue] < .05 criteria.
- 338 probes meeting the filter linked to a UniProt ID.
- 219 genes meeting the criterion linked to a GO term.
- 5221 Probes in this dataset
- 5100 Probes linked to a UniProt ID.
- 2475 Genes linked to a GO term.
The z score is based on an N of 2475 and a R of 219 distinct genes in the GO.
