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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 8866 in total

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
33.3333	2.3310728073120117	1	cullin-RING ubiquitin ligase complex	3	cellular component
			SCF ubiquitin ligase complex
	2.316990613937378	2	protein phosphatase type 2A activity	5	molecular function
	2.259546995162964	1	threonine-tRNA ligase activity	3
			threonyl-tRNA aminoacylation		biological process
	1.9814876317977905	2	regulation of immunoglobulin secretion	6
	1.7265567779541016	1	protein phosphatase type 1 complex	3	cellular component
	1.6965752840042114		beta-galactoside alpha-2,3-sialyltransferase activity		molecular function
	1.6583492755889893	2	selenocysteine incorporation	6	biological process
			translational readthrough
	1.6198676824569702	1	establishment of synaptic specificity at neuromuscular junction	3
			positive regulation of calcium ion transport
			positive regulation of ion transport
	1.4628015756607056		apical junction complex		cellular component
	1.4563519954681396		male pronucleus
	1.3346540927886963		arm morphogenesis		biological process
			embryonic arm morphogenesis
	1.2983962297439575		establishment of mitotic spindle localization
		2	cytokinesis during cell cycle	6
	1.2915130853652954	1	alpha(1,2)-fucosyltransferase activity	3	molecular function
			galactoside 2-alpha-L-fucosyltransferase activity
			kinetochore microtubule	4	cellular component
	1.2514674663543701		positive regulation of interleukin-4 biosynthetic process	3	biological process
			regulation of interleukin-4 biosynthetic process
	1.2257574796676636		methyl-CpG binding		molecular function
	1.1949561834335327		glyoxylate metabolic process		biological process
	1.192069411277771		nuclear RNA export factor complex		cellular component
	1.1431093215942383		protein kinase C inhibitor activity		molecular function
	1.1241697072982788	4	retinoid-X receptor activity	13
	1.1086714267730713	1	positive regulation of cAMP metabolic process	3	biological process
28.5714	2.463646113872528	2	glycerophosphodiester phosphodiesterase activity	8	molecular function
	1.9514372944831848		retinoic acid metabolic process	7	biological process
	1.2923074960708618		positive regulation of protein modification
25.0000	5.230461120605469	1	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	4	molecular function
	4.679882526397705		outward rectifier potassium channel activity
	4.046511650085449	2	establishment of nucleus localization	6	biological process
	3.313642740249634	1	triacylglycerol biosynthetic process	4
	2.723710060119629		chromocenter		cellular component
	2.611353635787964		peptide biosynthetic process		biological process
	2.3103933334350586		maintenance of protein localization in nucleus	5
	1.7584588527679443		L-cystine transporter activity	4	molecular function
			sulfur amino acid transporter activity
	1.7262773513793945		methylated-DNA-[protein]-cysteine S-methyltransferase activity
	1.6198676824569702		negative regulation of sequestering of calcium ion		biological process
			regulation of sensory perception of pain
			regulation of sequestering of calcium ion
			release of sequestered calcium ion into cytosol
			STAT protein nuclear translocation
	1.502064824104309	2	ceramide biosynthetic process	6
	1.4563519954681396	1	female pronucleus	4	cellular component

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.