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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 8866 in total

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

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.