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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Class
7	3.9735	2.267966568470001	164	biological process	transmembrane receptor protein tyrosine kinase signaling pathway
	3.6810	1.6151355107625325	184	cellular component	Golgi apparatus part
	3.5971	2.599970555305481	182	molecular function	amine receptor activity
	3.4682	3.243556241194407	191		alkali metal ion binding
	3.1746	1.8491697907447815	208	cellular component	synapse
	3.0928	2.506638288497925	238		microtubule
	3.0612	1.9925966064135234	216		cytoplasmic membrane-bound vesicle
					membrane-bound vesicle
	3.0303	1.3425244291623433	222	biological process	cell division
	2.2556	2.6377359429995217	315	molecular function	voltage-gated ion channel activity
	2.0833	1.9949067831039429	335	biological process	protein complex assembly
	2.0492	2.331825590133667	333	molecular function	carbohydrate binding
	2.0202	1.6523104111353557	337	biological process	response to DNA damage stimulus
	1.9608	2.2540424267450967	358		negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	1.8293	1.5113894144694011	388		amino acid and derivative metabolic process
	1.7595	1.5684048732121785	410	cellular component	cytosol
	1.5748	2.1708733439445496	421		organelle membrane
	1.5228	2.2601398825645447	464	biological process	monovalent inorganic cation transport
	1.4634	1.683560033639272	501		regulation of catalytic activity
8	4.2424	2.037709048816136	196	molecular function	anion transporter activity
	3.9773	2.6829177481787547	192	biological process	regulation of growth
	3.7234	1.8230999537876673	208		RNA splicing
	3.4146	1.6467143297195435	229		cell cycle phase
	3.3333	1.8456570080348425	249	molecular function	RNA polymerase II transcription factor activity
	2.5271	2.2348088707242693	321	biological process	nervous system development
	2.1605	2.6934666122709	379	cellular component	nucleoplasm part
	1.9663	1.6447297164372034	402		cell junction
	1.9608	2.2326475211552212	414	biological process	negative regulation of cellular metabolic process
	1.8421	2.158773183822632	428		response to endogenous stimulus
	1.7949	1.5929162161690849	463		amine metabolic process
	1.7157		484		nitrogen compound metabolic process
	1.6092	1.6290612050465174	527		regulation of a molecular function
	1.5748	1.4910563230514526	514		electron transport
9	6.3492	2.1655175536870956	142		protein amino acid dephosphorylation
	5.7143		158		dephosphorylation
	4.8000	2.9601402282714844	184	cellular component	chromatin
	4.1420	1.7680698462894984	221	molecular function	metallopeptidase activity
	3.8095	2.3925783783197403	230	biological process	enzyme linked receptor protein signaling pathway
	3.6145	2.5402226646741233	245	cellular component	chromosome
	3.4335	2.2164768129587173	264	biological process	organ morphogenesis
	3.1873	1.9443604201078415	295	molecular function	electrochemical potential-driven transporter activity
					porter activity
	2.9289	2.6086528982434953	318	biological process	inflammatory response
	2.8112	1.6669044835226876	327	molecular function	iron ion binding
	2.7888	1.4970425537654333	311		ATPase activity, coupled
	2.7778	2.043148085474968	323		transcription cofactor activity
	2.5078	2.4881605356931686	370		cation channel activity
		2.046714186668396		biological process	cell proliferation
	2.4922	2.8815125972032547	379		apoptosis
	2.4845		381		programmed cell death

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.