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