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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Class
6	3.0316067695617677	2.7174	231	microtubule-based process
	2.9956377029418944	2.9412	195	chromatin modification
	2.844642996788025	2.9070	206	nucleocytoplasmic transport
	2.7829527854919434	2.8249	211	visual perception
		2.8090	212	sensory perception of light stimulus
	2.745920252799988	1.1390	544	carbohydrate metabolic process
	2.4346015453338623	1.8051	325	negative regulation of transcription
	2.4153901100158692	2.0161	292	potassium ion transport
	2.329086923599243	5.1546	107	embryonic morphogenesis
	2.3127479553222656	1.4970	398	behavior
	1.9687834978103638	1.0870	559	cellular catabolic process
		0.8741	704	catabolic process
	1.9144784212112427	2.0661	272	positive regulation of cell proliferation
	1.8477724552154542	2.1930	287	cell-cell adhesion
	1.7971266508102417	2.1368	275	lipid biosynthetic process
	1.7727066993713378	2.4510	236	regulation of protein kinase activity
		2.3810	243	regulation of kinase activity
		2.3364	247	regulation of transferase activity
	1.7531960964202882		242	mRNA processing
		1.9841	289	mRNA metabolic process
	1.6556044340133667	2.6596	229	anion transport
	1.575242853164673	1.8727	314	amino acid metabolic process
	1.4007941484451294	2.3585	250	positive regulation of apoptosis
		2.3364	252	positive regulation of programmed cell death
	1.368695902824402	2.2321	260	chemical homeostasis
	1.3052469968795777	3.3333	170	regulation of cell differentiation
		2.0492	276	regulation of developmental process
7	2.6894871592521667	5.7692	117	muscle development
	2.267966568470001	3.9735	164	transmembrane receptor protein tyrosine kinase signaling pathway
	2.2601398825645447	1.5228	464	monovalent inorganic cation transport
	2.2540424267450967	1.9608	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	1.9949067831039429	2.0833	335	protein complex assembly
	1.683560033639272	1.4634	501	regulation of catalytic activity
	1.6523104111353557	2.0202	337	response to DNA damage stimulus
	1.632481078306834	4.7244	142	mitosis
	1.5113894144694011	1.8293	388	amino acid and derivative metabolic process
	1.3425244291623433	3.0303	222	cell division
8	2.6829177481787547	3.9773	192	regulation of growth
	2.2348088707242693	2.5271	321	nervous system development
	2.2326475211552212	1.9608	414	negative regulation of cellular metabolic process
	2.158773183822632	1.8421	428	response to endogenous stimulus
	1.8230999537876673	3.7234	208	RNA splicing
	1.6467143297195435	3.4146	229	cell cycle phase
	1.6290612050465174	1.6092	527	regulation of a molecular function
	1.5929162161690849	1.7949	463	amine metabolic process
		1.7157	484	nitrogen compound metabolic process
	1.4910563230514526	1.5748	514	electron transport
9	2.8815125972032547	2.4922	379	apoptosis
		2.4845	381	programmed cell death
	2.6086528982434953	2.9289	318	inflammatory response

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.