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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 8866 in total

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
7.3171	1.9710808197657268	4	53	hypersensitivity	biological process
				inflammatory response to antigenic stimulus
				type I hypersensitivity
	1.8127822875976562		48	synapse organization and biogenesis
7.1429	3.290644884109497	1	15	liver development
	1.9814876317977905		16	somatic diversification of immune receptors
			18	platelet activation
	1.4955823421478271		15	ureteric bud branching
			20	osteoblast differentiation
	1.3786529898643494	2	32	blood vessel development
	1.3475451469421387		30	ER-Golgi intermediate compartment	cellular component
	1.3020682334899902	1	15	phosphoprotein binding	molecular function
	1.2983962297439575		14	mitotic chromosome condensation	biological process
	1.2915130853652954			negative regulation of microtubule depolymerization
				regulation of microtubule depolymerization
	1.258076786994934		16	adult walking behavior
	1.2514674663543701		18	coreceptor activity	molecular function
	1.1949561834335327		19	glutathione metabolic process	biological process
	1.1833741068840027	2	29	positive regulation of growth
6.6667	5.84607458114624	1	17	chaperone binding	molecular function
	4.492823123931885		20	negative regulation of gene expression, epigenetic	biological process
	3.485576868057251		18	ephrin receptor activity	molecular function
	2.889312744140625	2	35	condensed chromosome	cellular component
	2.611353635787964	1	18	mitochondrial small ribosomal subunit
				organellar small ribosomal subunit
	2.4495278000831604	3	41	regulation of neuron apoptosis	biological process
	2.113001174396939	12	176	hormone activity	molecular function
	2.0561549067497253	2	33	protein amino acid ADP-ribosylation	biological process
	1.7584588527679443	1	16	lysosomal membrane	cellular component
	1.6685125231742859	2	33	sphingoid metabolic process	biological process
	1.4514795541763306	1	15	Golgi organization and biogenesis
	1.3786529898643494	2	34	vasculature development
	1.350217580795288	1	15	DNA N-glycosylase activity	molecular function
	1.3332858085632324		17	glycoprotein catabolic process	biological process
	1.3128347794214885	4	53	neurotransmitter transport
	1.3020682334899902	1	19	protein complex scaffold	molecular function
				receptor signaling complex scaffold activity
	1.3008167743682861		15	RNA polymerase II transcription mediator activity
	1.2915130853652954			negative regulation of microtubule polymerization or depolymerization	biological process
	1.2835599184036255		19	mammary gland development
	1.2520536184310913		20	cotranslational protein targeting to membrane
	1.2514674663543701		16	regulation of interleukin-2 biosynthetic process
	1.20618736743927			monovalent inorganic cation homeostasis
	1.1086714267730713		17	peptide hormone secretion
				peptide secretion
6.3492	2.1655175536870956	9	142	protein amino acid dephosphorylation
6.2500	5.835443019866943	2	27	single fertilization
	5.230461120605469	1	17	phosphoinositide 3-kinase complex	cellular component
	3.397643566131592		21	sarcoplasmic reticulum
	3.2791879177093506		18	specific transcriptional repressor activity	molecular function

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.