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	Accession	affected	Microarray Measured (#genes)

Results: HTML CSV LaTeX

Showing element 1 to 50 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
6.564077854156494	12.5000	1	8	cellular component	DNA-directed RNA polymerase III complex
	5.5556		19	biological process	transcription from RNA polymerase III promoter
	3.7037		31	cellular component	DNA-directed RNA polymerase complex
					nuclear DNA-directed RNA polymerase complex
	3.5714		32		RNA polymerase complex
	2.5000		51	molecular function	DNA-directed RNA polymerase activity
	0.9091		129		nucleotidyltransferase activity
5.84607458114624	20.0000		5	biological process	beta-tubulin folding
	14.2857		8		tubulin folding
	6.6667		17	molecular function	chaperone binding
5.835443019866943	100.0000		1	biological process	oocyte differentiation
				cellular component	cytoplasmic chromatin
	50.0000		2	biological process	positive regulation of meiosis
	33.3333		3		regulation of meiosis
	10.0000		12		regulation of exit from mitosis
	7.6923		15	molecular function	histone binding
	6.2500	2	27	biological process	single fertilization
	5.5556		30		fertilization
	4.7619	1		cellular component	nuclear chromatin
5.811023712158203	1.1628		104		cell surface
5.530585289001465	1.8868		63	molecular function	heat shock protein binding
5.326116561889648	5.2632		22	biological process	cellular respiration
	1.4085		82		energy derivation by oxidation of organic compounds
5.230461120605469	25.0000		4	molecular function	phosphatidylinositol-4,5-bisphosphate 3-kinase activity
	10.0000		11		1-phosphatidylinositol-3-kinase activity
					phosphoinositide 3-kinase activity
	9.0909		13	biological process	phosphoinositide phosphorylation
	8.3333		14		lipid phosphorylation
	6.2500		17	cellular component	phosphoinositide 3-kinase complex
	4.7619		25	molecular function	lipid kinase activity
	3.3333		35	biological process	lipid modification
	3.1250		37	molecular function	inositol or phosphatidylinositol kinase activity
	1.7857		76	biological process	phosphoinositide-mediated signaling
5.197549819946289	11.1111		11		hormone-mediated signaling
	3.4483		31	molecular function	hormone binding
	3.2258		32	biological process	fatty acid oxidation
	1.3158		85		response to hormone stimulus
5.013317108154297			105	molecular function	thiolester hydrolase activity
4.940977334976196	3.5714	3	73	cellular component	nuclear chromosome part
4.7113165855407715	50.0000	1	2	molecular function	pyruvate kinase activity
	1.9608		68	biological process	glycolysis
	1.6393		79		glucose catabolic process
	1.4706		89		hexose catabolic process
	1.4493		90		monosaccharide catabolic process
	1.3699		96		alcohol catabolic process
	1.1236		114		cellular carbohydrate catabolic process
	1.0638		121		carbohydrate catabolic process
	0.9615		130		glucose metabolic process
	0.6944		174		hexose metabolic process
	0.6623		182		monosaccharide 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.