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