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

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

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