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 451 to 500 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
1.7265567779541016	16.6667	1	6	ER overload response
	5.2632		21	ER-nuclear signaling pathway
				response to hydrogen peroxide
	3.8462		28	response to reactive oxygen species
1.714063827196757	2.0325	17	851	multicellular organismal development
1.7068785279989243	1.7699	10	545	cellular biosynthetic process
1.7028499245643616	4.1667	2	57	regulation of protein amino acid phosphorylation
			58	regulation of amino acid metabolic process
	3.3898		69	regulation of phosphorylation
	3.1746		73	regulation of phosphate metabolic process
				regulation of phosphorus metabolic process
1.6985642910003662	10.0000	1	10	neuromuscular synaptic transmission
1.6983322699864705	4.1667	4	92	hormone metabolic process
1.690700113773346	2.4390		183	pattern specification process
1.68887859582901	1.3699	3	189	chemotaxis
				taxis
1.6883443919095127	2.5172	13	514	cell-cell signaling
1.683560033639272	1.4634	7	501	regulation of catalytic activity
1.67010498046875	3.0000	3	114	Golgi vesicle transport
1.6685125231742859	7.4074	2	30	ceramide metabolic process
	6.6667		33	sphingoid metabolic process
	3.9216		58	sphingolipid metabolic process
1.6583492755889893	33.3333		6	selenocysteine incorporation
				translational readthrough
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
1.6372008621692657	0.9479	5	487	regulation of signal transduction
1.632481078306834	4.7244	7	142	mitosis
1.6290612050465174	1.6092	8	527	regulation of a molecular function
1.6198676824569702	33.3333	1	3	establishment of synaptic specificity at neuromuscular junction
				positive regulation of calcium ion transport
				positive regulation of ion transport
	25.0000		4	negative regulation of sequestering of calcium ion
				regulation of sensory perception of pain
				regulation of sequestering of calcium ion
				release of sequestered calcium ion into cytosol
				STAT protein nuclear translocation
	20.0000		5	positive regulation of vasoconstriction
				tyrosine phosphorylation of STAT protein
	16.6667		6	elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)
	14.2857		7	positive regulation of smooth muscle contraction
	12.5000		9	positive regulation of muscle contraction
	8.3333		13	regulation of vasoconstriction
	6.2500		16	activation of MAPKK activity
			17	regulation of calcium ion transport
	5.8824		21	regulation of smooth muscle contraction
	5.2632		22	negative regulation of neuron apoptosis
	4.7619		23	regulation of ion transport

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.