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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Average Regulation (ratio)	Class
6	5.1546	107	2.329086923599243	embryonic morphogenesis
	3.3333	170	1.3052469968795777	regulation of cell differentiation
	2.9412	195	2.9956377029418944	chromatin modification
	2.9070	206	2.844642996788025	nucleocytoplasmic transport
	2.8249	211	2.7829527854919434	visual perception
	2.8090	212		sensory perception of light stimulus
	2.7174	231	3.0316067695617677	microtubule-based process
	2.6596	229	1.6556044340133667	anion transport
	2.4510	236	1.7727066993713378	regulation of protein kinase activity
	2.3810	243		regulation of kinase activity
	2.3585	250	1.4007941484451294	positive regulation of apoptosis
	2.3364	242	1.7531960964202882	mRNA processing
		247	1.7727066993713378	regulation of transferase activity
		252	1.4007941484451294	positive regulation of programmed cell death
	2.2321	260	1.368695902824402	chemical homeostasis
	2.1930	287	1.8477724552154542	cell-cell adhesion
	2.1368	275	1.7971266508102417	lipid biosynthetic process
	2.0661	272	1.9144784212112427	positive regulation of cell proliferation
	2.0492	276	1.3052469968795777	regulation of developmental process
	2.0161	292	2.4153901100158692	potassium ion transport
	1.9841	289	1.7531960964202882	mRNA metabolic process
	1.8727	314	1.575242853164673	amino acid metabolic process
	1.8051	325	2.4346015453338623	negative regulation of transcription
	1.4970	398	2.3127479553222656	behavior
	1.1390	544	2.745920252799988	carbohydrate metabolic process
	1.0870	559	1.9687834978103638	cellular catabolic process
	0.8741	704		catabolic process
7	5.7692	117	2.6894871592521667	muscle development
	4.7244	142	1.632481078306834	mitosis
	3.9735	164	2.267966568470001	transmembrane receptor protein tyrosine kinase signaling pathway
	3.0303	222	1.3425244291623433	cell division
	2.0833	335	1.9949067831039429	protein complex assembly
	2.0202	337	1.6523104111353557	response to DNA damage stimulus
	1.9608	358	2.2540424267450967	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	1.8293	388	1.5113894144694011	amino acid and derivative metabolic process
	1.5228	464	2.2601398825645447	monovalent inorganic cation transport
	1.4634	501	1.683560033639272	regulation of catalytic activity
8	3.9773	192	2.6829177481787547	regulation of growth
	3.7234	208	1.8230999537876673	RNA splicing
	3.4146	229	1.6467143297195435	cell cycle phase
	2.5271	321	2.2348088707242693	nervous system development
	1.9608	414	2.2326475211552212	negative regulation of cellular metabolic process
	1.8421	428	2.158773183822632	response to endogenous stimulus
	1.7949	463	1.5929162161690849	amine metabolic process
	1.7157	484		nitrogen compound metabolic process
	1.6092	527	1.6290612050465174	regulation of a molecular function
	1.5748	514	1.4910563230514526	electron transport
9	6.3492	142	2.1655175536870956	protein amino acid dephosphorylation
	5.7143	158		dephosphorylation
	3.8095	230	2.3925783783197403	enzyme linked receptor protein signaling pathway

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.