Kevinmcgee Week 8

Digital Notebook

Part 1

Downloaded the Stanford Microarray Database data.
Made a new page called scaled_centered. Copied data from previous page, and calculated average ( =AVERAGE(B4:B5224) ) and standard deviation ( =STDEV(B4:B5224) )of them.
Made column for each called scaled_centered which subtracts average and divides by standard deviation ( =(B4-B$2)/B$3 ).
Made a new sheet called statistics. Copied data from previous page and took the average log fold change for each id value(=AVERAGE(B2:E2)). We then made a Tstat column which tells us if the scaled or centered average log ratio has change ( =AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(3) ) ). Finally, made a column for Pvalue ( =TDIST(ABS(R2),2,2) ).
Made page called forGenMAPP. On this page, pasted statistics page, then prepared for GenMAPP (number of decimal places, location of some column of information).

Part 2

121 Errors found
- My partner had 722 errors. The reason that he has more errors could be that he used an older version of the database, meaning that genes not found in his database could have been added since the last update.
The first 10 terms are as follows:
- biological adhesion
- biological regulation
- carbon utilization
- cell killing
- cellular component organization or biogenesis
- cellular component organization
- cell projection organization
- cell projection assembly
- flagellum organization
- pilus organization
1. - The lists are different from one another. This could be because I am using a database from 2012 while my buddy is using one from 2008
Gene associated Go terms
- VC0028
1. - metal ion binding
  - ion sulfur cluster binding
  - 4 iron, 4 sulfur cluster binding
  - catalytic activity
  - lyase activity
- VC0941
1. - transferase activity
  - glycine hydroxymethyltransferase activity
  - Catalyitic activity
  - pyridoxyl phosphate bonding
- VC0869
1. - ligase activity
  - catalytic activity
  - ATP binding
  - nucleotide binding
- VC0051
1. - catalytic activity
  - ATP binding
  - nucleotide binding
- VC0647
1. - transferase activity
  - nucleotidyltransferase activity
  - RNA binding
  - exribonuclease activity
  - mitochondriaon
- VC0468
1. - catalytic activity
  - ATP binding
  - nucleotide binding
- VC2350
1. - nothing was found
- VCA0583
1. - Outer membrane-bounded periplasmic space
- The lists are different from one another. This could be because I am using a database from 2012 while my buddy is using one from 2008
I clicked on the go term "metal ion bonding". Under that, I looked at the gene Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, which turned out to be decreased.
It was a component of the acetyl coenzyme A carboxylase complex.
We had a difference of the UniProt ID's of 338 while his was 339 and I had 219 genes linked to go terms while his had 291. I had 5221 probes in data set. I had 5100 linked to Uniprot while he had 4449 and I had 2475 linked to GO terms while he had 1990.The z score is based on an N of 2475 and a R of 219 distinct genes in the GO.
Top twenty filtered terms:
- arginine metabolic process
- cellular amino acid biosynthetic process
- purine nucleotide metabolic process
- cellular amino acid metabolic process
- purine nucleotide biosynthetic process
- nucleotide metabolic process
- nucleotide biosynthetic process
- ribonucleoside monophosphate biosynthetic process
- arginine biosynthetic process
- amine metabolic process
- extracellular region
- histidine biosynthetic process
- purine ribonucleotide biosynthetic process
- carbon-nitrogen ligase activity, with glutamine as amido-N-donor
- flagellum organization
- transporter activity
- carboxylic acid metabolic process
- transport
- thiamin pyrophosphate binding
- organic acid metabolic process
- amino acid transport