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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

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