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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 25 to 74 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Would Be Affected (#genes)	Class	Class
5.230461120605469	10.0000	11	1	1-phosphatidylinositol-3-kinase activity	molecular function
				phosphoinositide 3-kinase activity
	9.0909	13		phosphoinositide phosphorylation	biological process
	8.3333	14		lipid phosphorylation
	6.2500	17		phosphoinositide 3-kinase complex	cellular component
	4.7619	25		lipid kinase activity	molecular function
	3.3333	35		lipid modification	biological process
	3.1250	37		inositol or phosphatidylinositol kinase activity	molecular function
	1.7857	76		phosphoinositide-mediated signaling	biological process
5.197549819946289	11.1111	11		hormone-mediated signaling
	3.4483	31		hormone binding	molecular function
	3.2258	32		fatty acid oxidation	biological process
	1.3158	85		response to hormone stimulus
5.013317108154297		105		thiolester hydrolase activity	molecular function
4.940977334976196	3.5714	73	3	nuclear chromosome part	cellular component
4.7113165855407715	50.0000	2	1	pyruvate kinase activity	molecular function
	1.9608	68		glycolysis	biological process
	1.6393	79		glucose catabolic process
	1.4706	89		hexose catabolic process
	1.4493	90		monosaccharide catabolic process
	1.3699	96		alcohol catabolic process
	1.1236	114		cellular carbohydrate catabolic process
	1.0638	121		carbohydrate catabolic process
	0.9615	130		glucose metabolic process
	0.6944	174		hexose metabolic process
	0.6623	182		monosaccharide metabolic process
4.7064167857170105	1.9231	135	3	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	molecular function
	1.6807	151		oxidoreductase activity, acting on CH-OH group of donors
4.679882526397705	25.0000	4	1	outward rectifier potassium channel activity
	8.3333	13		delayed rectifier potassium channel activity
4.620415210723877	2.7027	40		protein amino acid N-linked glycosylation	biological process
4.601345539093018	1.0811	225	2	reproductive process
4.553711891174316	50.0000	2	1	parathyroid hormone receptor activity	molecular function
	3.5714	37		secretin-like receptor activity
4.506189823150635	5.8824	18		phagocytosis	biological process
4.492823123931885	6.6667	20		negative regulation of gene expression, epigenetic
	5.8824	19		nuclear membrane	cellular component
	2.2222	53		regulation of gene expression, epigenetic	biological process
4.407965660095215	14.2857	8		aldehyde dehydrogenase (NAD) activity	molecular function
	1.3333	100		neuropeptide signaling pathway	biological process
4.405977725982666	50.0000	2		GMP reductase activity	molecular function
				oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor
	1.5873	87		oxidoreductase activity, acting on NADH or NADPH
4.290065228939056	3.7037	66	2	histamine receptor activity
4.135706186294556	3.9474	90	4	nucleoplasm	cellular component
4.105485280354817	5.4545	80		humoral immune response	biological process
4.079947471618652	3.4483	32	1	insulin receptor signaling pathway
	3.3333			transport vesicle	cellular component
4.046511650085449	50.0000	3	2	nuclear migration	biological process
	33.3333		1	nuclear chromosome, telomeric region	cellular component

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.