Ky Roland - Revision history

Kyroland: /* Transcription Factors */

2018-03-27T14:39:16Z

‎Transcription Factors

2018-03-27T13:51:20Z

‎Transcription Factors

2018-03-20T14:58:18Z

2018-03-20T14:16:23Z

2018-03-20T13:48:19Z

2018-03-20T13:42:33Z

2018-03-20T13:40:16Z

‎Transcription Factors

2018-03-15T14:32:53Z

‎Transcription Factors

2018-03-15T13:44:47Z

‎Transcription Factors

2018-03-15T13:44:36Z

‎Transcription Factors

@@ Line 109: / Line 109: @@
 *Narrow down list using adjusted p-value (cutoff of .01) <br>
 *Rank gene list based on fold change (largest to smallest) <br>
-*Knockdown- moint mutation, mRNA is still in tact <br>
+*Input 3 ranked gene list into gene Venn <br>
 *RNAi- binds to mRNA and mRNA is destroyed; no protein is created <br>
 *Compare genes expressed in up regulated vs. down regulated genes and do GOrilla and WormBase analysis

@@ Line 111: / Line 111: @@
 *Knockdown- moint mutation, mRNA is still in tact <br>
 *RNAi- binds to mRNA and mRNA is destroyed; no protein is created <br>
-*Compare genes expressed in up regulated vs. down regulated genes and do GOrilla analysis
+*Compare genes expressed in up regulated vs. down regulated genes and do GOrilla and WormBase analysis

@@ Line 101: / Line 101: @@
 **sequencing library consists of 10 worms from roughly the same developmental stage <br>
-'''Pairwise COmparisons:'''
+'''Pairwise Comparisons:'''
-*WT vs Mutant <br>
+*WT vs Mutant [http://cbl-gorilla.cs.technion.ac.il/GOrilla/esword6j/GOResults.html GOrilla]<br>
-*WT vs. Knockdown <br>
+*WT vs. Knockdown [http://cbl-gorilla.cs.technion.ac.il/GOrilla/1asdvat3/GOResults.html GOrilla] <br>
 *Mutant vs. Knockdown <br>
 *Narrow down list using adjusted p-value (cutoff of .01) <br>
 *Rank gene list based on fold change (largest to smallest) <br>
 *Knockdown- moint mutation, mRNA is still in tact <br>
 *RNAi- binds to mRNA and mRNA is destroyed; no protein is created <br>

@@ Line 106: / Line 106: @@
 *Mutant vs. Knockdown <br>
-*Narrow down list using adjusted p-value <br>
+*Narrow down list using adjusted p-value (cutoff of .01) <br>
 *Rank gene list based on fold change (largest to smallest) <br>
-*Knockdown- moint mutation, mRNA is still in tact
+*Knockdown- moint mutation, mRNA is still in tact <br>
-*RNAi- binds to mRNA and mRNA is destroyed; no protein is created
+*RNAi- binds to mRNA and mRNA is destroyed; no protein is created <br>

← Older revision		Revision as of 13:48, 20 March 2018
Line 108:		Line 108:
	*Narrow down list using adjusted p-value <br>		*Narrow down list using adjusted p-value <br>
	*Rank gene list based on fold change (largest to smallest) <br>		*Rank gene list based on fold change (largest to smallest) <br>
		+	*Knockdown- moint mutation, mRNA is still in tact
		+	*RNAi- binds to mRNA and mRNA is destroyed; no protein is created

← Older revision		Revision as of 13:42, 20 March 2018
Line 105:		Line 105:
	*WT vs. Knockdown <br>		*WT vs. Knockdown <br>
	*Mutant vs. Knockdown <br>		*Mutant vs. Knockdown <br>
		+
		+	*Narrow down list using adjusted p-value <br>
		+	*Rank gene list based on fold change (largest to smallest) <br>

@@ Line 92: / Line 92: @@
 **nhr-25 is essential, therefore we have to knockdown the gene as opposed to knocking it out<br>
 **transiently knocked down by RNAi- molting and vulval defects<br>
 **nhr-25(ku217) mutant- molting and vulval defect<br>
 ***leucine to proline point mutation in the D<br>
@@ Line 99: / Line 100: @@
 *identification of nhr-25 regulated genes <br>
 **sequencing library consists of 10 worms from roughly the same developmental stage <br>

← Older revision		Revision as of 14:32, 15 March 2018
Line 77:		Line 77:

	What GO terms are associated with NR5A1? <br>		What GO terms are associated with NR5A1? <br>
		+
		+	'''nhr-25: Model Transcription Factor''' <br>
		+	*Background<br>
		+	**an important developmental regulator<br>
		+	**known phenotypes and tools<br>
		+	**mammalian orthologs<br>
		+
		+	*NHR-25<br>
		+	**transcription factor of large family: nuclear hormone receptors<br>
		+	**expressed in seam and vulval cells throughout development <br>
		+	**'''human orthologs''': SF-1 and LRH-1; and '''Drosophila''': Ftz-F1<br>
		+
		+	*Mutants to identify regulated genes<br>
		+	**nhr-25 is essential, therefore we have to knockdown the gene as opposed to knocking it out<br>
		+	**transiently knocked down by RNAi- molting and vulval defects<br>
		+	**nhr-25(ku217) mutant- molting and vulval defect<br>
		+	***leucine to proline point mutation in the D<br>
		+	NA biding domain<br>
		+	***mutant has reduced DNA binding<br>
		+
		+	*identification of nhr-25 regulated genes <br>
		+	**sequencing library consists of 10 worms from roughly the same developmental stage <br>

@@ Line 69: / Line 69: @@
 == '''Transcription Factors''' ==
 Start with Gene search in [https://www.ncbi.nlm.nih.gov/gene/2516 NCBI].<br>
 Where is this expressed? (all 4 data sets) <br>
 Human conditions when mutated? <br>
 How many proteins does NR5A1 interact with? <br>
 What GO terms are associated with NR5A1? <br>