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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8866 in total

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

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.