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