Heart Disease and Virtual Pulldown - Revision history

Krivi: /* Heart disease proteins */

2026-10-01T12:41:57Z

Heart disease proteins

← Older revision		Revision as of 13:41, 1 October 2026
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	=== Heart disease proteins ===		=== Heart disease proteins ===
	We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect\| Atrioventricular septal defect]''' ("~~AACM~~"):		We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect\| Atrioventricular septal defect]''' ("ASD"):

	<pre>		<pre>

2026-10-01T12:41:35Z

Heart disease proteins

← Older revision		Revision as of 13:41, 1 October 2026
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	=== Heart disease proteins ===		=== Heart disease proteins ===
	We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect\|Atrioventricular septal defect]''' ("AACM"):		We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect\| Atrioventricular septal defect]''' ("AACM"):

	<pre>		<pre>

2026-10-01T12:41:23Z

Heart disease proteins

← Older revision		Revision as of 13:41, 1 October 2026
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	=== Heart disease proteins ===		=== Heart disease proteins ===
	We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect]''' ("AACM"):		We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect\|Atrioventricular septal defect]''' ("AACM"):

	<pre>		<pre>

2026-10-01T11:47:56Z

Heart disease proteins

← Older revision		Revision as of 12:47, 1 October 2026
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	=== Heart disease proteins ===		=== Heart disease proteins ===
	We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect~~\|Abnormal atrioventricular canal morphology~~]''' ("AACM"):		We'll start out with a set of proteins known to be involved in '''[https://en.wikipedia.org/wiki/Atrioventricular_septal_defect]''' ("AACM"):

	<pre>		<pre>

2025-09-26T10:19:58Z

Visualizing networks

← Older revision		Revision as of 11:19, 26 September 2025
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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	'''REPORT QUESTION #2":		'''REPORT QUESTION #2":
	* ~~Plot~~ the graph created by filtering with confidence score 0.2. Indicate which nodes are seed notes and which are neighbours.		* Use ggraph to plot the graph created by filtering with confidence score 0.2. Indicate which nodes are seed notes and which are neighbours.

	=== Functional classification ===		=== Functional classification ===

2025-09-26T10:19:39Z

Exercise on "Virtual Pulldowns"

← Older revision		Revision as of 11:19, 26 September 2025
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	</pre>		</pre>

	2: Extract all connections with a confidence score >= 0.2 and use igraph to create a graph with the data		2: Extract all connections with a confidence score >= 0.2 and use igraph to create a graph with the (data via the graph_from_dataframe() function). No plotting needed now.

2025-09-20T16:26:42Z

Exercise on "Virtual Pulldowns"

← Older revision		Revision as of 17:26, 20 September 2025
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	# The PPI database we will use is InWeb:		# The PPI database we will use is InWeb:
	load(file='/home/projects/22140/~~inweb_reduced~~.Rdata')		load(file='/home/projects/22140/exercise4.Rdata')
	</pre>		</pre>

2025-09-19T07:12:08Z

Functional classification

← Older revision		Revision as of 08:12, 19 September 2025
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	=== Functional classification ===		=== Functional classification ===
	Use loivant clustering with resolution = 0.4 to find sub-clusters in the network. For the 2-3 largest clusters do gene-set overrepressentation analysis with fora(). What background do you need to use? (you already have all information needed to ~~descided~~ this ~~- no information is missing~~)		Use loivant clustering with resolution = 0.4 to find sub-clusters in the network. For the 2-3 largest clusters do gene-set overrepressentation analysis with fora(). What background do you need to use? (you already have all the information needed to decide and use this background)

	<pre>		<pre>

2025-09-19T07:11:33Z

Functional classification

← Older revision		Revision as of 08:11, 19 September 2025
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	=== Functional classification ===		=== Functional classification ===
	Use loivant clustering with resolution = 0.4 to find sub-clusters in the network. For the 2-3 largest clusters do gene-set overrepressentation analysis with fora().		Use loivant clustering with resolution = 0.4 to find sub-clusters in the network. For the 2-3 largest clusters do gene-set overrepressentation analysis with fora(). What background do you need to use? (you already have all information needed to descided this - no information is missing)

	<pre>		<pre>

2025-09-19T07:10:11Z

Human diseases / virtual pulldown exercise

← Older revision		Revision as of 08:10, 19 September 2025
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	*# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins"		*# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins"
	*# Finding tightly connected clusters in larger networks		*# Finding tightly connected clusters in larger networks
	*# Using R to extract, analyze and visualize (sub)networks		*# Using R to extract, analyze, interpret and visualize (sub)networks

	== Introduction ==		== Introduction ==