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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

Would Be Affected (#genes)	% Affected Genes	Class	Average Regulation (ratio)	Class Size (#genes)	Class
8	2.5271	biological process	2.2348088707242693	321	nervous system development
	2.1605	cellular component	2.6934666122709	379	nucleoplasm part
	1.9663		1.6447297164372034	402	cell junction
	1.9608	biological process	2.2326475211552212	414	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	cellular component	2.9601402282714844	184	chromatin
	4.1420	molecular function	1.7680698462894984	221	metallopeptidase activity
	3.8095	biological process	2.3925783783197403	230	enzyme linked receptor protein signaling pathway
	3.6145	cellular component	2.5402226646741233	245	chromosome
	3.4335	biological process	2.2164768129587173	264	organ morphogenesis
	3.1873	molecular function	1.9443604201078415	295	electrochemical potential-driven transporter activity
					porter activity
	2.9289	biological process	2.6086528982434953	318	inflammatory response
	2.8112	molecular function	1.6669044835226876	327	iron ion binding
	2.7888		1.4970425537654333	311	ATPase activity, coupled
	2.7778		2.043148085474968	323	transcription cofactor activity
	2.5078	biological process	2.046714186668396	370	cell proliferation
		molecular function	2.4881605356931686		cation channel activity
	2.4922	biological process	2.8815125972032547	379	apoptosis
	2.4845			381	programmed cell death
	2.3460	molecular function	2.4995227009058	380	magnesium ion binding
	2.2222		1.4970425537654333	385	ATPase activity
	2.1390	biological process	2.1474349200725555	432	cell motility
	2.0202		2.1150057166814804	460	negative regulation of metabolic process
	1.8248	molecular function	2.2257004976272583	497	olfactory receptor activity
	1.7677	cellular component	2.317225064550127	510	extracellular space
	1.6327	biological process	1.9312101155519485	570	carboxylic acid metabolic process
	1.6227			573	organic acid metabolic process
	1.0458	cellular component	2.1532876193523407	896	mitochondrion
10	6.0000	molecular function	2.116744134161207	171	phosphoprotein phosphatase activity
	4.7059	biological process	2.4113256633281708	216	response to freezing
		molecular function			ice binding
					water binding
	4.6784	biological process		217	homoiothermy
	4.4444			226	thermoregulation
	3.9823	molecular function	2.116744134161207	261	phosphoric monoester hydrolase activity
	3.0928		2.506679137547811	331	transcriptional activator activity
	2.9801	biological process	2.3975469536251492	338	positive regulation of transcription
	2.9197		2.4850547462701797	358	response to wounding
	2.8939		2.3975469536251492	347	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	2.8754	molecular function	2.523834652370877	363	identical protein binding
	2.5000	biological process	3.175950493131365	416	establishment and/or maintenance of chromatin architecture
	2.4561			422	DNA packaging
	2.3936	molecular function	1.6601282623079088	437	cytoskeletal protein binding

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.