Paul - Revision history

Pabrennan: /* Paul's Notes */

2017-04-13T14:57:28Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-04-11T14:54:37Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-04-04T14:57:29Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-04-04T14:18:41Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-03-30T14:57:47Z

‎Paul's Notes

Pabrennan at 14:55, 23 March 2017

2017-03-23T14:55:37Z

Pabrennan: /* Paul's Notes */

2017-03-16T14:50:31Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-03-16T14:49:14Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-02-28T15:58:32Z

‎Paul's Notes

Pabrennan: /* Paul's Notes */

2017-02-21T15:45:00Z

‎Paul's Notes

← Older revision		Revision as of 14:57, 13 April 2017
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	Producing GO graphs with important terms (over fold enrichment value of 2). I made graphs with the GO terms (MF, BP, and CC) for all downregulated (MT/PT) genes, but not upregulated genes. Should I plan on putting all the genes into the graphs? How much info is too much? Any way to consolidate the data would be very helpful. I could make a larger graph including both positive and negative		Producing GO graphs with important terms (over fold enrichment value of 2). I made graphs with the GO terms (MF, BP, and CC) for all downregulated (MT/PT) genes, but not upregulated genes. Should I plan on putting all the genes into the graphs? How much info is too much? Any way to consolidate the data would be very helpful. I could make a larger graph including both positive and negative
		+
		+	4/13/17
		+
		+	Need to produce GO graphs for upregulated MT/PT, as well as graphs for upregulated and downregulated M WT / P WT (as a control). I will be able to hand pick genes (or more easily: pathways) which appear enriched in both the trisomic test and the control test. This shows which pathways are especially upregulated in the trisomic mouse model versus pathways which are normally differentially regulated between the two genetic backgrounds. This is useful because the goal of our project is to characterize the gene expression differences between the paternal trisomic and maternal trisomic mice.
		+
		+	For continued analysis: Complete same GO analysis between Maternal/Paternal WT

← Older revision		Revision as of 14:54, 11 April 2017
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	Upregulated in Maternal Trisomic vs Paternal Trisomic		Upregulated in Maternal Trisomic vs Paternal Trisomic
		+
		+
		+	4/11/17
		+
		+	Producing GO graphs with important terms (over fold enrichment value of 2). I made graphs with the GO terms (MF, BP, and CC) for all downregulated (MT/PT) genes, but not upregulated genes. Should I plan on putting all the genes into the graphs? How much info is too much? Any way to consolidate the data would be very helpful. I could make a larger graph including both positive and negative

@@ Line 118: / Line 118: @@
 Steps:
-. MT vs PT DeSeq2 Filtered for p-value <0.001
+. MT vs PT DeSeq2 Filtered for p-value <0.01 and LFC > 0  (separate upregulated and downregulated genes)
 . Remove Ensembl ID decimals
 . Input into MGI to change ensembl to common gene name
 . input list to Gene Ontology Consortium
-Results
+Results (see Gene Ontology Folder)
 Upregulated in Maternal Trisomic vs Paternal Trisomic

← Older revision		Revision as of 14:18, 4 April 2017
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	Workflow to get set of genes that are all upregulated --> GO will figure out if they organize into common functions and such. keep working on this		Workflow to get set of genes that are all upregulated --> GO will figure out if they organize into common functions and such. keep working on this
		+
		+
		+	----
		+	4/4/17
		+
		+	Gene Ontology Investigation: Do the significantly differentially expressed genes between maternal trisomic and paternal trisomic have gene organizational patterns?
		+
		+	Steps:
		+
		+	1. MT vs PT DeSeq2 Filtered for p-value <0.001
		+	2. Remove Ensembl ID decimals
		+	3. Input into MGI to change ensembl to common gene name
		+	4. input list to Gene Ontology Consortium
		+
		+	Results
		+
		+	Upregulated in Maternal Trisomic vs Paternal Trisomic
		+
		+	[[File:Example.jpg]]

← Older revision		Revision as of 14:57, 30 March 2017
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	3. Merge this comparison with the known gene information.		3. Merge this comparison with the known gene information.
	4. Compare gene expression differences. Some differences could be due to parent-specific imprinting.		4. Compare gene expression differences. Some differences could be due to parent-specific imprinting.
		+
		+
		+	GO pathway enrichment analysis
		+
		+	Workflow to get set of genes that are all upregulated --> GO will figure out if they organize into common functions and such. keep working on this

@@ Line 1: / Line 1: @@
 == Paul's Notes ==
@@ Line 83: / Line 87: @@
 Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear
 lamina interactions during differentiation. Mol. Cell 38, 603–613 (2010).

← Older revision		Revision as of 14:50, 16 March 2017
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	[[File:Paternal Tris/Dis Chr19.png\|200px]]		[[File:Paternal Tris/Dis Chr19.png\|200px]]

		+	[[File:Paternal Tris/Dis Chr19.png\|200px]]

	Papers cited by Letourneau with LAD data:		Papers cited by Letourneau with LAD data:

← Older revision		Revision as of 14:49, 16 March 2017
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	Chromosome 10 Differential Expression		Chromosome 10 Differential Expression

−	[[File:~~Screen Shot 2017-02-21 at 10~~.41.~~46 AM~~.png\|200px]]	+	[[File:Maternal Tris/Dis Chrom10.png\|200px]]
		+
		+	[[File:Maternal Tris/Dis Chrom19.png\|200px]]
		+
		+	[[File:Maternal Tris/Dis Chrom 15.png\|200px]]
		+
		+	[[File:Paternal Tris/Dis Chr15.png\|200px]]
		+
		+	[[File:Paternal Tris/Dis Chr10.png\|200px]]
		+
		+	[[File:Paternal Tris/Dis Chr19.png\|200px]]

← Older revision		Revision as of 15:58, 28 February 2017
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	[[File:Screen Shot 2017-02-21 at 10.41.46 AM.png\|200px]]		[[File:Screen Shot 2017-02-21 at 10.41.46 AM.png\|200px]]
		+
		+
		+	Papers cited by Letourneau with LAD data:
		+
		+	Guelen, L. et al. Domain organization of human chromosomes revealed by
		+	mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).
		+
		+	Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear
		+	lamina interactions during differentiation. Mol. Cell 38, 603–613 (2010).

← Older revision		Revision as of 15:45, 21 February 2017
Line 62:		Line 62:
	Chromosome 10 Differential Expression		Chromosome 10 Differential Expression

−	[[File:Screen Shot 2017-02-21 at 10.41.46 AM.png]]	+	[[File:Screen Shot 2017-02-21 at 10.41.46 AM.png\|200px]]