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