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