MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20)

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Class
6	12.1951	1.8410587787628174	47	molecular function	protein serine/threonine phosphatase activity
	8.0645	1.864961290359497	71		tubulin binding
	6.0976	1.8525358200073243	96		endonuclease activity
	5.4945	2.046875333786011	110		chromatin binding
	5.4545	3.243556241194407	118		potassium ion binding
	5.1546	2.329086923599243	107	biological process	embryonic morphogenesis
	4.5113	1.7925277551015217	142	molecular function	calmodulin binding
	3.3333	1.3052469968795777	170	biological process	regulation of cell differentiation
	3.1250	1.3853561878204346	197	cellular component	vacuole
	2.9412	2.9956377029418944	195	biological process	chromatin modification
	2.9070	2.844642996788025	206		nucleocytoplasmic transport
	2.8249	2.7829527854919434	211		visual perception
	2.8090		212		sensory perception of light stimulus
	2.7174	3.0316067695617677	231		microtubule-based process
	2.6596	1.6556044340133667	229		anion transport
	2.4510	1.7727066993713378	236		regulation of protein kinase activity
	2.3810		243		regulation of kinase activity
	2.3585	1.5512258529663085	261	molecular function	transferase activity, transferring glycosyl groups
		1.4007941484451294	250	biological process	positive regulation of apoptosis
	2.3364	1.7727066993713378	247		regulation of transferase activity
		1.7531960964202882	242		mRNA processing
		1.4007941484451294	252		positive regulation of programmed cell death
	2.3256	1.4126896858215332	269	molecular function	neurotransmitter receptor activity
	2.2936		273		neurotransmitter binding
	2.2422	2.3990859508514406	256	cellular component	soluble fraction
	2.2321	1.368695902824402	260	biological process	chemical homeostasis
	2.1930	1.8477724552154542	287		cell-cell adhesion
	2.1368	1.7971266508102417	275		lipid biosynthetic process
	2.0661	1.9144784212112427	272		positive regulation of cell proliferation
	2.0492	1.3052469968795777	276		regulation of developmental process
	2.0161	2.4153901100158692	292		potassium ion transport
	1.9841	1.7531960964202882	289		mRNA metabolic process
	1.8727	1.575242853164673	314		amino acid metabolic process
	1.8051	2.4346015453338623	325		negative regulation of transcription
	1.4970	2.3127479553222656	398		behavior
	1.4925	1.5197211980819703	400	molecular function	GTPase regulator activity
	1.4620	1.7229081869125367	377	cellular component	cell projection
	1.3369	2.9851186752319334	448	molecular function	lipid binding
	1.1390	2.745920252799988	544	biological process	carbohydrate metabolic process
	1.0870	1.9687834978103638	559		cellular catabolic process
	0.8741		704		catabolic process
7	5.7692	2.6894871592521667	117		muscle development
	5.6180	1.8354295253753663	116	molecular function	metalloendopeptidase activity
	4.7244	1.632481078306834	142	biological process	mitosis
	4.3796	1.82427982489268	165	molecular function	nuclease activity
	4.2017	1.4174904584884644	156		ATPase activity, coupled to transmembrane movement of substances
	4.1322	1.5547808408737183	172		heme binding
					tetrapyrrole binding
		1.4174904584884644	158		ATPase activity, coupled to movement of substances
			159		hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.