Alondra Vega: Week 12

Analyzing and Interpreting STEM results

• I chose Profile 9 because we were recommended to choose a profile that was either up- or down regulated in the first three time points. This profile was down-refulated for the first three time points. This is interesting because the cell decided that it needed to turn off those genes to be able to survive during cold shock.
• There were 248 genes assigned to this profile.
• There were 42.1 genes expected.
• The p-value is 1.2Ε-110.
• There are 95 GO terms associated with this profile that have a p-value of less than 0.05.
• In the corrected p-value there are 8 GO terms associated with this profile that have a p-value of less than 0.05.

GO terms and their descriptions

1. glutamine family amino acid biosynthetic process
2. oxidoreductase activity
3. small molecule biosynthetic process
4. carboxylic acid biosynthetic process
5. organic acid biosynthetic process
6. oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
7. actin cortical patch
8. pentose metabolic process
9. cytoplasm
10. cytoskeletal protein binding

• The glutamine family amino acid biosynthetic process deals with chemical reactions and processeses that result in the formation of amino acids and of the glutamine family; this includes arginine, glutamate, glutamine,and proline. As we have learned in class, glutamate and glutamine are part of the nitrogen metabolism and it can be said that yeast are decreasing the expression of these genes because they do not need as much nitrogen in their cold shock phase, as they would in regular basis.

Keep in mind that the dataset you studied was one where the Gln3 transcription factor was deleted.  
Gln3, if it was present, would normally activate genes involved in nitrogen metabolism.  
So if Gln3 is absent, genes that would normally be up-regulated are down-regulated instead.  
This is what we were hoping to see in this experiment.  
— Kam D. Dahlquist 23:21, 27 April 2011 (EDT)

Oxidoreductase activity deals with the catalysis of oxidative-reductive reactions. This is a process in which one substrate acts as the electron donor and the other acts as the electron acceptor. The fact that the genes in this category are down regulated may be because the cold is not allowing the cell to produce the oxygen that it needs, thus it is not going to waste its resources in keeping these genes on when it is not using them.

This term is referring to enzymes that perform oxidation and reduction reactions.
These reactions do not necessarily involve oxygen.  For example, some of the reactions in the nitrogen  
metabolism pathway are oxidation/reduction reactions.  — Kam D. Dahlquist 23:32, 27 April 2011 (EDT)

The small molecule biosynthetic process focuses on the reactions and pathways that result in the formation of small molecules. When an environmental stress is introduced to a cell, the cell wants to limit the resources it is going to use and what it uses them on. Producing small molecules may not be the most important or crucial for survival, when the cell needs to focus on inducing the most important genes needed during cold shock. Carboxylic acid biosynthetic process deals with reactions and pathways that build carboxylic acids. This goes back to the fact that the cell disrupts both the nitrogen and carbon cycles. Carboxylic acids are affected because they contain carbon and the cell might not be producing any. Organic acid biosynthetic process deals with any carbon reactions. I think that since cold shock has a great effect in carbon producing, all reaction with carbon will be down-regulated.

These terms are probably related to each other.  Carboxylic acids are small molecules and they are also 
organic acids.  Amino acids (the building blocks of proteins) contain carboxyl groups so this could be 
referring to amino acids.  Keep in mind that you chose a cluster where the genes were down-regulated, not 
induced.  If the cell has shut down protein synthesis because of the cold, then it would not need to make 
amino acids either.  — Kam D. Dahlquist 23:39, 27 April 2011 (EDT)

Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, which is similar to oxidative reductase, but this is more specific. This refers to the usage of NAD and NADP.

See my response above, especially since NAD and NADP are used in the nitrogen metabolism pathway.  — Kam D. Dahlquist 23:41, 27 April 2011 (EDT) 

Actin cortical patch deals with an actin containing structure found in the plasma membrane at the sites of endocytosis. I think that this is down-regulated during cold shock because the cell membrane becomes weak.

I wouldn't say that the membrane becomes weak; it becomes less fluid.  — Kam D. Dahlquist 23:41, 27 April 2011 (EDT)

Pentose metabolic process deals with chains of reactions that have 5 or more carbons. The fact that carbon is reduced during cold shock, then it explains why all of the processes with carbon are showing up.

Pentose sugars have exactly 5 carbons, not 5 or more.  This is a pretty general term, it could be referring
to the cell using 5 carbon sugars instead of glucose (a 6 carbon sugar) as an energy source, or it could 
refer to ribose metabolism (a 5 carbon sugar and part of RNA).  Without knowing which specific genes to 
this term is referring, it's hard to say.  — Kam D. Dahlquist 23:50, 27 April 2011 (EDT)

Cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. When cold is introduced t the cell, they cell gets "rid" of unnecessary items, thus I feel that the cytoplasm is one of those.

Remember what I said in class when interpreting this term for Sarah.  This term is just too broad to be
meaningful.  — Kam D. Dahlquist 23:50, 27 April 2011 (EDT)

Cytoskeletal protein binding deals with the interaction of selectively and non-covalently with any protein component of any cytoskeleton. This may be down regulated during cold shock because the cell is focusing on keeping other structures strong, that is ignoring the small filaments and microfilaments.

Cytoskeletal components (microtubules) are also used to separate the chromosomes during mitosis.  If the
cell has stopped dividing, it would not need these.  — Kam D. Dahlquist 23:50, 27 April 2011 (EDT)

Results from Yeastract

Top Ten transcription Factors

1. STE12 with a 39.1%.
2. RAP1 with a 24.6%.
3. FHL1 with a 16.9%.
4. YAP6 with a 16.5%.
5. YAP5 with a 14.5%.
6. CIN5 with a 13.7%.
7. SKO1 with a 13.3%.
8. SKN7 with a 11.7%.
9. SOK2 with a 12.9%.
10. PHD1 with a 10.1%.

GLN3

• GLN3 does show up on the list and it regulates about 5.6% of the genes.
• It regulates 14 genes.
• List: HIS4; CHA1; YDR210w; YEL007w; GCN4; TMT1; PMA1; ARG4; YHI9; DAL3; ARG3; LAP4; ARG1; ZEO1

Adding genes to the network

1. STE12: I would like to add it to the network since it regulates many of the genes in my cluster. Also it is known to be involved in mating and growth processes. This might show us if the cell is replicating or not.
2. YAP5: I would like to add it because its molecular function is RNA polymerase II and I feel that anything that has to do with regulating the ribosome is important, since it carries the transcription factors.
3. SKO1: It is known to be involved in osmotic and oxidative stress responses. It will be interesting to see how it reacts in cold shock, if it even has a relevant reaction.
4. SOK2: It deals with the signal transduction pathway and the cyclic AMP, which correlates to carbon metabolism.
5. SKN7: It is known to react to heat shock, so it can be another gene that we can compare to another environmental stress and how it behaves in different scenarios.