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 551 to 600 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
1.5134246349334717	1.9608	2	117	response to bacterium
1.5113894144694011	1.8293	7	388	amino acid and derivative metabolic process
1.502064824104309	25.0000	2	6	ceramide biosynthetic process
	20.0000	1	7	sphingoid biosynthetic process
1.4992291927337646	16.6667		6	platelet-derived growth factor receptor signaling pathway
	0.7752		152	regulation of small GTPase mediated signal transduction
1.4977699518203735	1.7857	4	206	induction of apoptosis
	1.7751		207	induction of programmed cell death
1.4955823421478271	100.0000	1	1	positive regulation of astrocyte differentiation
	50.0000		2	regulation of astrocyte differentiation
	20.0000		5	positive regulation of glial cell differentiation
				positive regulation of gliogenesis
	16.6667		6	positive regulation of osteoblast differentiation
	12.5000		8	regulation of glial cell differentiation
				regulation of gliogenesis
			9	regulation of osteoblast differentiation
	11.1111			positive regulation of ossification
			10	cardiac cell differentiation
	10.0000			positive regulation of bone remodeling
	8.3333		13	bone mineralization
				epithelial to mesenchymal transition
			14	BMP signaling pathway
	7.1429		15	ureteric bud branching
			20	osteoblast differentiation
	5.8824			cartilage development
	4.0000		27	regulation of ossification
	3.8462		29	odontogenesis (sensu Vertebrata)
	3.3333		32	regulation of bone remodeling
	3.1250		36	odontogenesis
	2.4390		46	cell fate commitment
	2.3256		47	branching morphogenesis of a tube
	2.1277		52	morphogenesis of a branching structure
			53	transmembrane receptor protein serine/threonine kinase signaling pathway
	2.0000		59	tube morphogenesis
	1.5385		78	biomineral formation
				ossification
1.4910563230514526	1.5748	8	514	electron transport
1.4838887453079224	2.0833	1	57	ATP synthesis coupled proton transport
				energy coupled proton transport, down electrochemical gradient
	1.9608		63	ATP biosynthetic process
				nucleoside phosphate metabolic process
	1.8182		69	ATP metabolic process
	1.5625		78	purine nucleoside triphosphate biosynthetic process
				purine ribonucleoside triphosphate biosynthetic process
	1.5385		79	ribonucleoside triphosphate biosynthetic process
	1.4925		83	nucleoside triphosphate biosynthetic process
	1.4706		84	purine ribonucleoside triphosphate metabolic process
	1.4493		85	purine nucleoside triphosphate metabolic process
				ribonucleoside triphosphate metabolic process
			88	group transfer coenzyme metabolic process

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.