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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 8866 in total

% Affected Genes	Class	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
33.3333	SCF ubiquitin ligase complex	2.3310728073120117	1	3	cellular component
	selenocysteine incorporation	1.6583492755889893	2	6	biological process
	threonine-tRNA ligase activity	2.259546995162964	1	3	molecular function
	threonyl-tRNA aminoacylation				biological process
	Toll binding	3.5441412925720215			molecular function
	translational readthrough	1.6583492755889893	2	6	biological process
28.5714	glycerophosphodiester phosphodiesterase activity	2.463646113872528		8	molecular function
	positive regulation of protein modification	1.2923074960708618		7	biological process
	retinoic acid metabolic process	1.9514372944831848
25.0000	adenohypophysis development	1.1086714267730713	1	4
	AP-1 adaptor complex	1.3020682334899902		5	cellular component
	arachidonic acid metabolic process	1.1809606552124023		4	biological process
	carotenoid biosynthetic process	1.4308764934539795		5
	ceramide biosynthetic process	1.502064824104309	2	6
	chromocenter	2.723710060119629	1	4	cellular component
	embryonic eye morphogenesis	1.20923912525177			biological process
	establishment of nucleus localization	4.046511650085449	2	6
	establishment of spindle localization	1.2983962297439575	1	4
	female pronucleus	1.4563519954681396			cellular component
	ferric-chelate reductase activity	1.2010211944580078			molecular function
	L-cystine transporter activity	1.7584588527679443
	maintenance of protein localization in nucleus	2.3103933334350586		5	biological process
	methylated-DNA-[protein]-cysteine S-methyltransferase activity	1.7262773513793945		4	molecular function
	mitotic G2 checkpoint	1.4563519954681396			biological process
	negative regulation of sequestering of calcium ion	1.6198676824569702
	outward rectifier potassium channel activity	4.679882526397705			molecular function
	oxidized base lesion DNA N-glycosylase activity	1.350217580795288
	oxidized purine base lesion DNA N-glycosylase activity
	peptide biosynthetic process	2.611353635787964			biological process
	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	5.230461120605469			molecular function
	positive regulation of cyclic nucleotide metabolic process	1.1086714267730713			biological process
	positive regulation of exocytosis	1.2165690660476685		5
	positive regulation of T-helper cell differentiation	1.2514674663543701		4
	protein phosphatase type 1 activity	1.2769564390182495		5	molecular function
	regulation of cardiac muscle cell proliferation	1.3346540927886963		4	biological process
	regulation of global transcription from RNA polymerase II promoter	1.3008167743682861
	regulation of sensory perception of pain	1.6198676824569702
	regulation of sequestering of calcium ion
	regulation of T-helper 2 cell differentiation	1.2514674663543701
	release of sequestered calcium ion into cytosol	1.6198676824569702
	STAT protein nuclear translocation
	sulfur amino acid transporter activity	1.7584588527679443			molecular function
	sulfurtransferase activity	1.1953918933868408		5
	terpenoid biosynthetic process	1.4308764934539795			biological process
	tetraterpenoid biosynthetic process
	thyroid hormone generation	1.192122220993042	2	7
	thyroid hormone receptor coactivator activity	1.1241697072982788	3	11	molecular function
	triacylglycerol biosynthetic process	3.313642740249634	1	4	biological process
20.0000	3-chloroallyl aldehyde dehydrogenase activity	1.20923912525177		7	molecular function
	antigen processing and presentation of endogenous peptide antigen	1.765833854675293	2	12	biological process

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.