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)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

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