Difference between revisions of "Vkuehn Week 15"

Latest revision as of 11:56, 11 December 2013

P-value less than 0.05: 5303
P-value less that 0.01: 2130
P-value less that 0.001: 317
P-value less that 0.0001: 0
Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
Average log fold change of > 0.25 and p < 0.05: 2861
Average log fold change of < -0.25 and p < 0.05: 2431

For exact procedure reference Vkuehn Week 13 or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
The colors were assigned to the two main criterion
- Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored blue
- Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored purple

PermuteP (in column O) less than 0.05

Came up with 6 results for increased
Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)

PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100

Came up with 8 results for decreased
Found a lot that have to do with catabolic process.
"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"
aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds

Ran genmapp and waiting for results to be generated

@@ Line 12: / Line 12: @@
 *Average log fold change of < -0.25 and p < 0.05: 2431
 ===GenMAPP Expression Dataset Manager===
-*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
+*For exact procedure reference [[Vkuehn Week 13]] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
 * The colors were assigned to the two main criterion
 **Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''