Kasey E. O'Connor Week 12 Journal

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(layout edit)
(STEMquestions)
Line 3: Line 3:
===Questions===
===Questions===
#Why did you select this profile? In other words, why was it interesting to you?
#Why did you select this profile? In other words, why was it interesting to you?
-
#*
+
#*I chose profile 45 because there was an large increase in gene expression within the first two time periods. I was curious to find out what genes are found on this profile, and what systems they are related to within the cell.
#How many genes belong to this profile?
#How many genes belong to this profile?
-
#*
+
#*286
#How many genes were expected to belong to this profile?
#How many genes were expected to belong to this profile?
-
#*
+
#*34.8
#What is the p value for the enrichment of genes in this profile?
#What is the p value for the enrichment of genes in this profile?
-
#*
+
#*6.2x10<sup>-165</sup>
#How many GO terms are associated with this profile at p < 0.05?
#How many GO terms are associated with this profile at p < 0.05?
-
#*
+
#*152
#How many GO terms are associated with this profile with a corrected p value < 0.05?
#How many GO terms are associated with this profile with a corrected p value < 0.05?
-
#*
+
#*16
#Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?
#Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?
 +
#*
 +
#*
 +
#*
 +
#*
 +
#*
 +
#*
 +
#*
 +
#*
 +
#*
#*
#*
==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==
==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==

Revision as of 12:39, 9 April 2013

Contents

Clustering and Gene Ontology Analysis with STEM

Process

Questions

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose profile 45 because there was an large increase in gene expression within the first two time periods. I was curious to find out what genes are found on this profile, and what systems they are related to within the cell.
  2. How many genes belong to this profile?
    • 286
  3. How many genes were expected to belong to this profile?
    • 34.8
  4. What is the p value for the enrichment of genes in this profile?
    • 6.2x10-165
  5. How many GO terms are associated with this profile at p < 0.05?
    • 152
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 16
  7. Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?

Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes

Process

Questions

  1. What are the top 10 transcription factors in your results? List them on your wiki page with the percent of the genes in your cluster that they each regulate.
  2. Are Cin5, Gln3, Hmo1, and Zap1 on the list? What percentage of the genes in the cluster does they each regulate? How many genes does they each regulate?
  3. Which transcription factors do you want to add to the model and why?

Powerpoint File

Useful Links

Personal tools