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)	affected	Class	Class	Class Size (#genes)	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class	Class Size (#genes)
33.3333	4.046511650085449	1	nuclear membrane organization and biogenesis	3
	3.367248058319092	2	positive regulation of viral life cycle	5
			regulation of antiviral response
	2.5450799465179443	1	intercellular junction maintenance	3
	2.259546995162964		threonyl-tRNA aminoacylation
	1.9814876317977905	2	regulation of immunoglobulin secretion	6
	1.6583492755889893		selenocysteine incorporation
			translational readthrough
	1.6198676824569702	1	establishment of synaptic specificity at neuromuscular junction	3
			positive regulation of calcium ion transport
			positive regulation of ion transport
	1.3346540927886963		arm morphogenesis
			embryonic arm morphogenesis
	1.2983962297439575		establishment of mitotic spindle localization
		2	cytokinesis during cell cycle	6
	1.2514674663543701	1	positive regulation of interleukin-4 biosynthetic process	3
			regulation of interleukin-4 biosynthetic process
	1.1949561834335327		glyoxylate metabolic process
	1.1086714267730713		positive regulation of cAMP metabolic process
28.5714	1.9514372944831848	2	retinoic acid metabolic process	7
	1.2923074960708618		positive regulation of protein modification
25.0000	4.046511650085449		establishment of nucleus localization	6
	3.313642740249634	1	triacylglycerol biosynthetic process	4
	2.611353635787964		peptide biosynthetic process
	2.3103933334350586		maintenance of protein localization in nucleus	5
	1.6198676824569702		negative regulation of sequestering of calcium ion	4
			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	mitotic G2 checkpoint	4
	1.4308764934539795		carotenoid biosynthetic process	5
			terpenoid biosynthetic process
			tetraterpenoid biosynthetic process
	1.3346540927886963		regulation of cardiac muscle cell proliferation	4
	1.3008167743682861		regulation of global transcription from RNA polymerase II promoter
	1.2983962297439575		establishment of spindle localization
	1.2514674663543701		positive regulation of T-helper cell differentiation
			regulation of T-helper 2 cell differentiation
	1.2165690660476685		positive regulation of exocytosis	5
	1.20923912525177		embryonic eye morphogenesis	4
	1.192122220993042	2	thyroid hormone generation	7
	1.1809606552124023	1	arachidonic acid metabolic process	4
	1.1086714267730713		adenohypophysis development
			positive regulation of cyclic nucleotide metabolic process
20.0000	5.84607458114624		beta-tubulin folding	5
	3.367248058319092	2	regulation of viral genome replication	10
	3.0503673553466797	1	substrate-bound cell migration, cell extension	5
	2.7504823207855225		centrosome duplication

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.