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

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.