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

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class	Class Size (#genes)
2.0103142169805674	16	2.5048	homeostatic process	623
		2.3679	regulation of biological quality	660
1.9949067831039429	7	2.0833	protein complex assembly	335
1.9786490954850848	26	1.8357	biosynthetic process	1417
1.9769652134332902	48	2.0945	multicellular organismal process	2294
1.9759902954101562	17	2.1417	proteolysis	800
1.9687834978103638	6	1.0870	cellular catabolic process	559
		0.8741	catabolic process	704
1.9621534997766668	25	2.4123	positive regulation of cellular process	1036
1.9346576482057571	11	1.6701	generation of precursor metabolites and energy	629
1.9312101155519485	9	1.6327	carboxylic acid metabolic process	570
		1.6227	organic acid metabolic process	573
1.9144784212112427	6	2.0661	positive regulation of cell proliferation	272
1.8924930147502734	27	3.5604	cell cycle process	746
1.8484420895576477	23	4.3573	regulation of progression through cell cycle	535
		4.3197	regulation of cell cycle	539
1.8477724552154542	6	2.1930	cell-cell adhesion	287
1.8413102626800537	10	2.2670	RNA processing	448
1.8383450422968184	17	2.1407	biological adhesion	806
			cell adhesion
1.8230999537876673	8	3.7234	RNA splicing	208
1.7971266508102417	6	2.1368	lipid biosynthetic process	275
1.7727066993713378		2.4510	regulation of protein kinase activity	236
		2.3810	regulation of kinase activity	243
		2.3364	regulation of transferase activity	247
1.7531960964202882			mRNA processing	242
		1.9841	mRNA metabolic process	289
1.714063827196757	17	2.0325	multicellular organismal development	851
1.7068785279989243	10	1.7699	cellular biosynthetic process	545
1.6883443919095127	13	2.5172	cell-cell signaling	514
1.683560033639272	7	1.4634	regulation of catalytic activity	501
1.6556044340133667	6	2.6596	anion transport	229
1.6538901064130995	10	1.9737	regulation of cell proliferation	527
1.6523104111353557	7	2.0202	response to DNA damage stimulus	337
1.6467143297195435	8	3.4146	cell cycle phase	229
1.632481078306834	7	4.7244	mitosis	142
1.6290612050465174	8	1.6092	regulation of a molecular function	527
1.6056334376335144	14	3.0303	cell cycle	458
1.5929162161690849	8	1.7949	amine metabolic process	463
		1.7157	nitrogen compound metabolic process	484
1.575242853164673	6	1.8727	amino acid metabolic process	314
1.5113894144694011	7	1.8293	amino acid and derivative metabolic process	388
1.4910563230514526	8	1.5748	electron transport	514
1.4007941484451294	6	2.3585	positive regulation of apoptosis	250
		2.3364	positive regulation of programmed cell death	252
1.368695902824402		2.2321	chemical homeostasis	260
1.3425244291623433	7	3.0303	cell division	222
1.3052469968795777	6	3.3333	regulation of cell differentiation	170
		2.0492	regulation of developmental process	276

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.