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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8866 in total

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class	Class
4.7064167857170105	3	1.9231	135	molecular function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
		1.6807	151		oxidoreductase activity, acting on CH-OH group of donors
4.679882526397705	1	25.0000	4		outward rectifier potassium channel activity
		8.3333	13		delayed rectifier potassium channel activity
4.620415210723877		2.7027	40	biological process	protein amino acid N-linked glycosylation
4.601345539093018	2	1.0811	225		reproductive process
4.553711891174316	1	50.0000	2	molecular function	parathyroid hormone receptor activity
		3.5714	37		secretin-like receptor activity
4.506189823150635		5.8824	18	biological process	phagocytosis
4.492823123931885		6.6667	20		negative regulation of gene expression, epigenetic
		5.8824	19	cellular component	nuclear membrane
		2.2222	53	biological process	regulation of gene expression, epigenetic
4.407965660095215		14.2857	8	molecular function	aldehyde dehydrogenase (NAD) activity
		1.3333	100	biological process	neuropeptide signaling pathway
4.405977725982666		50.0000	2	molecular function	GMP reductase activity
					oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor
		1.5873	87		oxidoreductase activity, acting on NADH or NADPH
4.290065228939056	2	3.7037	66		histamine receptor activity
4.135706186294556	4	3.9474	90	cellular component	nucleoplasm
4.105485280354817		5.4545	80	biological process	humoral immune response
4.079947471618652	1	3.4483	32		insulin receptor signaling pathway
		3.3333		cellular component	transport vesicle
4.046511650085449		33.3333	3	biological process	nuclear membrane organization and biogenesis
				cellular component	nuclear chromosome, telomeric region
		12.5000	9	biological process	mitotic spindle organization and biogenesis
		7.6923	16	cellular component	condensed nuclear chromosome
		5.0000	23		chromosome, telomeric region
		2.3256	56		nuclear envelope
	2	50.0000	3	biological process	nuclear migration
		25.0000	6		establishment of nucleus localization
4.037245273590088	1	14.2857	7		transmembrane receptor protein tyrosine phosphatase signaling pathway
		5.5556	18	molecular function	transmembrane receptor protein phosphatase activity
					transmembrane receptor protein tyrosine phosphatase activity
3.9968204498291016		1.7857	72		vascular endothelial growth factor receptor activity
		1.0309	119		GPI anchor binding
3.9418493509292603	3	1.5385	172		cysteine-type peptidase activity
3.9217323064804077	2	40.0000	5	biological process	embryonic skeletal morphogenesis
		18.1818	13		skeletal morphogenesis
3.895843982696533	1	1.0309	109		Wnt receptor signaling pathway
3.8507699966430664	2	100.0000	2	molecular function	arylamine N-acetyltransferase activity
		4.5455	52		N-acetyltransferase activity
		4.0000	61		N-acyltransferase activity
		3.7736	63		acetyltransferase activity
3.8397669792175293	1	5.0000	21	cellular component	nuclear matrix
3.819567561149597	4	3.2258	133	biological process	regulation of cell growth
3.8173599243164062	1	2.9412	39		transcription initiation from RNA polymerase II promoter
		1.7857	68		transcription initiation
3.789476911226908	4	4.4118	80	molecular function	structural constituent of cell wall
3.749711751937866	1	12.5000	10		glutathione peroxidase activity
	2	5.2632	31		selenium binding

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.