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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)
1.6198676824569702	4.5455	peptidyl-tyrosine phosphorylation	1	23
	4.3478	protein import into nucleus, translocation		27
	4.1667	peptidyl-tyrosine modification		25
		protein kinase C activation		27
	3.0303	caspase activation		38
		regulation of muscle contraction		42
	2.7778	positive regulation of caspase activity		43
	2.2222	regulation of caspase activity		54
	1.7544	activation of protein kinase activity		63
	1.7241	positive regulation of hydrolase activity		69
	1.3158	peptidyl-amino acid modification		84
1.6164775490760803	9.0909	lymphocyte proliferation	2	24
		mononuclear cell proliferation
	1.7857	lymphocyte activation		123
1.6134718656539917	1.3514	epidermis development	1	92
1.6074604988098145	4.3478	tetracycline transport		28
	4.1667	response to antibiotic		30
	3.7037	drug transport		33
1.6066848039627075	100.0000	osmosensory signaling pathway		1
	14.2857	regulation of cell volume		8
	10.0000	response to osmotic stress		11
	4.5455	response to mechanical stimulus		29
1.6056334376335144	3.0303	cell cycle	14	458
1.6005929708480835	2.7027	steroid metabolic process	5	184
1.598192811012268	2.5000	detection of stimulus during sensory perception	1	48
	1.4286	detection of stimulus		84
1.5929162161690849	1.7949	amine metabolic process	8	463
	1.7157	nitrogen compound metabolic process		484
1.581991195678711	3.2787	amino acid transport	2	62
1.5804486274719238	7.6923	peroxisome organization and biogenesis	1	13
1.575242853164673	1.8727	amino acid metabolic process	6	314
1.5708750486373901	100.0000	caudate nucleus development	1	1
		putamen development
1.5622674822807312	13.3333	fibroblast growth factor receptor signaling pathway	2	15
1.5580885410308838	5.0000	GPI anchor biosynthetic process	1	21
	4.7619	GPI anchor metabolic process		22
	4.0000	phosphoinositide biosynthetic process		27
	2.8571	glycerophospholipid biosynthetic process		40
	1.6393	phospholipid biosynthetic process		69
	1.3699	membrane lipid biosynthetic process		83
1.5568770170211792	1.2579	male gamete generation	3	205
		spermatogenesis
	1.0989	gamete generation		235
1.5545271039009094	0.9524	tissue development	2	248
1.5518782138824463	2.5974	intracellular protein transport across a membrane		91
1.545079529285431	3.2787	regulation of secretion		72
1.541499376296997	1.3699	chloride transport	1	80
1.5287119547526042	4.1667	amine transport	3	74
1.523066798845927	1.2346	DNA repair		278
1.5134246349334717	2.2222	defense response to bacterium	2	108

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.