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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 5007 in total

Class  : biological process

Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	% Affected Genes	Class
6.564077854156494	1	19	5.5556	transcription from RNA polymerase III promoter
5.84607458114624		5	20.0000	beta-tubulin folding
		8	14.2857	tubulin folding
5.835443019866943		1	100.0000	oocyte differentiation
		2	50.0000	positive regulation of meiosis
		3	33.3333	regulation of meiosis
		12	10.0000	regulation of exit from mitosis
	2	27	6.2500	single fertilization
		30	5.5556	fertilization
5.326116561889648	1	22	5.2632	cellular respiration
		82	1.4085	energy derivation by oxidation of organic compounds
5.230461120605469		13	9.0909	phosphoinositide phosphorylation
		14	8.3333	lipid phosphorylation
		35	3.3333	lipid modification
		76	1.7857	phosphoinositide-mediated signaling
5.197549819946289		11	11.1111	hormone-mediated signaling
		32	3.2258	fatty acid oxidation
		85	1.3158	response to hormone stimulus
4.7113165855407715		68	1.9608	glycolysis
		79	1.6393	glucose catabolic process
		89	1.4706	hexose catabolic process
		90	1.4493	monosaccharide catabolic process
		96	1.3699	alcohol catabolic process
		114	1.1236	cellular carbohydrate catabolic process
		121	1.0638	carbohydrate catabolic process
		130	0.9615	glucose metabolic process
		174	0.6944	hexose metabolic process
		182	0.6623	monosaccharide metabolic process
4.620415210723877		40	2.7027	protein amino acid N-linked glycosylation
4.601345539093018	2	225	1.0811	reproductive process
4.506189823150635	1	18	5.8824	phagocytosis
4.492823123931885		20	6.6667	negative regulation of gene expression, epigenetic
		53	2.2222	regulation of gene expression, epigenetic
4.407965660095215		100	1.3333	neuropeptide signaling pathway
4.105485280354817	4	80	5.4545	humoral immune response
4.079947471618652	1	32	3.4483	insulin receptor signaling pathway
4.046511650085449		3	33.3333	nuclear membrane organization and biogenesis
		9	12.5000	mitotic spindle organization and biogenesis
	2	3	50.0000	nuclear migration
		6	25.0000	establishment of nucleus localization
4.037245273590088	1	7	14.2857	transmembrane receptor protein tyrosine phosphatase signaling pathway
3.9217323064804077	2	5	40.0000	embryonic skeletal morphogenesis
		13	18.1818	skeletal morphogenesis
3.895843982696533	1	109	1.0309	Wnt receptor signaling pathway
3.819567561149597	4	133	3.2258	regulation of cell growth
3.8173599243164062	1	39	2.9412	transcription initiation from RNA polymerase II promoter
		68	1.7857	transcription initiation
3.721451759338379	2	53	4.4444	chromatin remodeling
3.7029240131378174	1	2	50.0000	myoblast migration
		10	11.1111	thymus development

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.