Difference between revisions of "Vkuehn Week 15"

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*Average log fold change of < -0.25 and p < 0.05: 2431
 
*Average log fold change of < -0.25 and p < 0.05: 2431
 
===GenMAPP Expression Dataset Manager===
 
===GenMAPP Expression Dataset Manager===
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*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols  
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*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
 
* 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'''
 
**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'''
 
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''
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=='''12/7/13'''==
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===GO Terms Analysed using MAPPFinder===
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*Filtered Z Score (in column N) greater than 2
 +
PermuteP (in column O) less than 0.05
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:*Came up with 6 results for increased
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:*Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
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:*: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)
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:*: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)
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*Filtered Z Score (in column N) greater than 2
 +
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
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:*Came up with 8 results for decreased
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:*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"
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:*:aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
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:*:cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds
 +
 
===GenMAPP Finder===
 
===GenMAPP Finder===
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ran genmapp and waiting for results to be generated
+
Ran genmapp and waiting for results to be generated
 +
 
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{{Template:Vkuehn}}
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[[Category: Journal Entry]]

Latest revision as of 11:56, 11 December 2013

Contents

[edit] ELECTRONIC NOTEBOOK

[edit] 12/5/13

[edit] Sanity Check

  • 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

[edit] GenMAPP Expression Dataset Manager

[edit] 12/7/13

[edit] GO Terms Analysed using MAPPFinder

  • Filtered Z Score (in column N) greater than 2

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)
  • Filtered Z Score (in column N) greater than 2

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

[edit] GenMAPP Finder

Ran genmapp and waiting for results to be generated

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