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)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	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)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)
1.7265567779541016	ER overload response	16.6667	1	6
	ER-nuclear signaling pathway	5.2632		21
	response to hydrogen peroxide
	response to reactive oxygen species	3.8462		28
1.714063827196757	multicellular organismal development	2.0325	17	851
1.7068785279989243	cellular biosynthetic process	1.7699	10	545
1.7028499245643616	regulation of amino acid metabolic process	4.1667	2	58
	regulation of phosphate metabolic process	3.1746		73
	regulation of phosphorus metabolic process
	regulation of phosphorylation	3.3898		69
	regulation of protein amino acid phosphorylation	4.1667		57
1.6985642910003662	neuromuscular synaptic transmission	10.0000	1	10
1.6983322699864705	hormone metabolic process	4.1667	4	92
1.690700113773346	pattern specification process	2.4390		183
1.68887859582901	chemotaxis	1.3699	3	189
	taxis
1.6883443919095127	cell-cell signaling	2.5172	13	514
1.683560033639272	regulation of catalytic activity	1.4634	7	501
1.67010498046875	Golgi vesicle transport	3.0000	3	114
1.6685125231742859	ceramide metabolic process	7.4074	2	30
	sphingoid metabolic process	6.6667		33
	sphingolipid metabolic process	3.9216		58
1.6583492755889893	selenocysteine incorporation	33.3333		6
	translational readthrough
1.6556044340133667	anion transport	2.6596	6	229
1.6538901064130995	regulation of cell proliferation	1.9737	10	527
1.6523104111353557	response to DNA damage stimulus	2.0202	7	337
1.6467143297195435	cell cycle phase	3.4146	8	229
1.6372008621692657	regulation of signal transduction	0.9479	5	487
1.632481078306834	mitosis	4.7244	7	142
1.6290612050465174	regulation of a molecular function	1.6092	8	527
1.6198676824569702	activation of MAPKK activity	6.2500	1	16
	activation of protein kinase activity	1.7544		63
	caspase activation	3.0303		38
	elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	16.6667		6
	establishment of synaptic specificity at neuromuscular junction	33.3333		3
	negative regulation of neuron apoptosis	5.2632		22
	negative regulation of sequestering of calcium ion	25.0000		4
	peptidyl-amino acid modification	1.3158		84
	peptidyl-tyrosine modification	4.1667		25
	peptidyl-tyrosine phosphorylation	4.5455		23
	positive regulation of calcium ion transport	33.3333		3
	positive regulation of caspase activity	2.7778		43
	positive regulation of hydrolase activity	1.7241		69
	positive regulation of ion transport	33.3333		3
	positive regulation of muscle contraction	12.5000		9
	positive regulation of smooth muscle contraction	14.2857		7
	positive regulation of vasoconstriction	20.0000		5
	protein import into nucleus, translocation	4.3478		27
	protein kinase C activation	4.1667

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.