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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

% Affected Genes	Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#genes)	Class	Class
12.1951	6	1.8410587787628174	47	protein serine/threonine phosphatase activity	molecular function
8.0645		1.864961290359497	71	tubulin binding
6.6667	12	2.113001174396939	176	hormone activity
6.3492	9	2.1655175536870956	142	protein amino acid dephosphorylation	biological process
6.0976	6	1.8525358200073243	96	endonuclease activity	molecular function
6.0000	10	2.116744134161207	171	phosphoprotein phosphatase activity
5.7692	7	2.6894871592521667	117	muscle development	biological process
5.7143	9	2.1655175536870956	158	dephosphorylation
5.6180	7	1.8354295253753663	116	metalloendopeptidase activity	molecular function
5.4945	6	2.046875333786011	110	chromatin binding
5.4545		3.243556241194407	118	potassium ion binding
5.1546		2.329086923599243	107	embryonic morphogenesis	biological process
5.0000	11	2.6329536702897816	226	response to cold
4.8000	9	2.9601402282714844	184	chromatin	cellular component
4.7619	13	2.455523896217346	270	GTPase activity	molecular function
4.7244	7	1.632481078306834	142	mitosis	biological process
4.7059	10	2.4113256633281708	216	ice binding	molecular function
				response to freezing	biological process
				water binding	molecular function
4.6784			217	homoiothermy	biological process
4.5113	6	1.7925277551015217	142	calmodulin binding	molecular function
4.4554	11	2.6329536702897816	249	response to temperature stimulus	biological process
4.4444	10	2.4113256633281708	226	thermoregulation
4.3796	7	1.82427982489268	165	nuclease activity	molecular function
4.3573	23	1.8484420895576477	535	regulation of progression through cell cycle	biological process
4.3197			539	regulation of cell cycle
4.2424	8	2.037709048816136	196	anion transporter activity	molecular function
4.2017	7	1.4174904584884644	156	ATPase activity, coupled to transmembrane movement of substances
4.1420	9	1.7680698462894984	221	metallopeptidase activity
4.1322	7	1.5547808408737183	172	heme binding
				tetrapyrrole binding
		1.4174904584884644	158	ATPase activity, coupled to movement of substances
			159	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
4.1270	17	2.3509053725462694	417	GTP binding
4.0541	14	2.12662406762441	341	phosphoric ester hydrolase activity
4.0268		2.7959404488404593	360	protein dimerization activity
4.0248	17	2.3509053725462694	427	guanyl nucleotide binding
3.9823	10	2.116744134161207	261	phosphoric monoester hydrolase activity
3.9773	8	2.6829177481787547	192	regulation of growth	biological process
3.9735	7	2.267966568470001	164	transmembrane receptor protein tyrosine kinase signaling pathway
3.8095	9	2.3925783783197403	230	enzyme linked receptor protein signaling pathway
3.7234	8	1.8230999537876673	208	RNA splicing
3.6810	7	1.6151355107625325	184	Golgi apparatus part	cellular component
3.6145	9	2.5402226646741233	245	chromosome
3.5971	7	2.599970555305481	182	amine receptor activity	molecular function
3.5604	27	1.8924930147502734	746	cell cycle process	biological process
3.4700	16	2.8238616314801304	472	chromosomal part	cellular component
3.4682	7	3.243556241194407	191	alkali metal ion binding	molecular function
3.4335	9	2.2164768129587173	264	organ morphogenesis	biological process
3.4272	36	2.3974582254886627	1038	transcription factor 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.