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	Microarray Measured (#genes)	affected	Accession

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

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.