Nick Rohacz: Week 12


 * 1) I selected profile 2 because it starts off down regulated at the starting time points then the gene becomes up regulated in the later time points, meaning it was not necessary for any immediate cold response, but it was turned on once the cell thought it was going to be in a cold environment for an extended time period.
 * 2) 41.8 genes belong to this profile.
 * 3) 71.0 genes were expected to belong to this profile.
 * 4) P-value is 2.0E-5, this is significant.
 * 5) Seven GO were associated with the profile when p < 0.05.
 * 6) No GO terms were associated with a corrected p value < 0.05.
 * 7) Only seven terms for p value < 0.05, both normal and corrected.
 * 8) *glucose metabolic process - The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides
 * 9) *hexose metabolic process - The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
 * 10) *monosaccharide metabolic process - The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
 * 11) *mitotic cell cycle - Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
 * 12) *carbohydrate metabolic process - The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
 * 13) *cell cycle process - A cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
 * 14) *cytoskeleton organization - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
 * 15) A majority of the terms that are significant deal with the breakdown of sugars and the creation of energy. As well as many energy demanding reactions such as the mitotic cell cycle. These processes require large amounts of energy that are most likely being stored instead of broken down immediately so that the cell will be able to survive for an extended period in cold conditions, instead of dying from lack of energy.
 * 16) Top 10 Transcription Factors
 * 17) *Ste12p 35.2 %
 * 18) *Rap1p 22.5 %
 * 19) *Phd1p 15.5 %
 * 20) *Sok2p 12.7 %
 * 21) *Fhl1p 12.7 %
 * 22) *Mbp1p 12.7 %
 * 23) *Skn7p 12.7 %
 * 24) *Swi4p 12.7 %
 * 25) *Yap5p 12.7 %
 * 26) *Xbp1p 12.7 %
 * 27) Yes it is, but not in the top 10. Gln3p 5.6%, four genes are regulated, they are FEN2, RRG1, DAL3, YNR068c
 * 28) Ste12p, Rap1p, Phd1p, Sok2p, Fhl1p because these are the top 5 transcription found to regulate the breakdown of sugars and creation of energy in gene profile 2.

Nicholas A. Rohacz 01:33, 12 April 2011 (EDT)