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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
2.0103142169805674	2.5048	16	623	homeostatic process
	2.3679		660	regulation of biological quality
1.9949067831039429	2.0833	7	335	protein complex assembly
1.9786490954850848	1.8357	26	1417	biosynthetic process
1.9769652134332902	2.0945	48	2294	multicellular organismal process
1.9759902954101562	2.1417	17	800	proteolysis
1.9687834978103638	1.0870	6	559	cellular catabolic process
	0.8741		704	catabolic process
1.9621534997766668	2.4123	25	1036	positive regulation of cellular process
1.9346576482057571	1.6701	11	629	generation of precursor metabolites and energy
1.9312101155519485	1.6327	9	570	carboxylic acid metabolic process
	1.6227		573	organic acid metabolic process
1.9144784212112427	2.0661	6	272	positive regulation of cell proliferation
1.8924930147502734	3.5604	27	746	cell cycle process
1.8484420895576477	4.3573	23	535	regulation of progression through cell cycle
	4.3197		539	regulation of cell cycle
1.8477724552154542	2.1930	6	287	cell-cell adhesion
1.8413102626800537	2.2670	10	448	RNA processing
1.8383450422968184	2.1407	17	806	biological adhesion
				cell adhesion
1.8230999537876673	3.7234	8	208	RNA splicing
1.7971266508102417	2.1368	6	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
1.714063827196757	2.0325	17	851	multicellular organismal development
1.7068785279989243	1.7699	10	545	cellular biosynthetic process
1.6883443919095127	2.5172	13	514	cell-cell signaling
1.683560033639272	1.4634	7	501	regulation of catalytic activity
1.6556044340133667	2.6596	6	229	anion transport
1.6538901064130995	1.9737	10	527	regulation of cell proliferation
1.6523104111353557	2.0202	7	337	response to DNA damage stimulus
1.6467143297195435	3.4146	8	229	cell cycle phase
1.632481078306834	4.7244	7	142	mitosis
1.6290612050465174	1.6092	8	527	regulation of a molecular function
1.6056334376335144	3.0303	14	458	cell cycle
1.5929162161690849	1.7949	8	463	amine metabolic process
	1.7157		484	nitrogen compound metabolic process
1.575242853164673	1.8727	6	314	amino acid metabolic process
1.5113894144694011	1.8293	7	388	amino acid and derivative metabolic process
1.4910563230514526	1.5748	8	514	electron transport
1.4007941484451294	2.3585	6	250	positive regulation of apoptosis
	2.3364		252	positive regulation of programmed cell death
1.368695902824402	2.2321		260	chemical homeostasis
1.3425244291623433	3.0303	7	222	cell division
1.3052469968795777	3.3333	6	170	regulation of cell differentiation
	2.0492		276	regulation of developmental process

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.