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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class	Class Size (#genes)
2.523834652370877	2.8754	10	identical protein binding	molecular function	363
2.5149934005737307	2.3063	34	intracellular non-membrane-bound organelle	cellular component	1485
			non-membrane-bound organelle
2.506679137547811	3.0928	10	transcriptional activator activity	molecular function	331
2.506638288497925		7	microtubule	cellular component	238
2.5005394551489086	1.8711	21	cellular developmental process	biological process	1118
2.4995227009058	2.3460	9	magnesium ion binding	molecular function	380
2.4881605356931686	2.5078		cation channel activity		370
2.4850547462701797	2.9197	10	response to wounding	biological process	358
2.4829982866843543	3.0968	28	phosphate metabolic process		890
			phosphorus metabolic process
2.470501118236118	3.0405	52	protein modification process		1721
	2.9393		biopolymer modification		1780
2.46775693159837	2.9680	15	regulation of transcription from RNA polymerase II promoter		499
2.455523896217346	4.7619	13	GTPase activity	molecular function	270
2.453812837600708	1.9231	11	translation	biological process	552
2.4517960273302517	2.2569	15	protein kinase activity	molecular function	672
2.4479837675352356	2.9529	43	post-translational protein modification	biological process	1442
2.4382004340489707	2.2514	16	sensory perception		732
	2.2181		neurological process		741
2.4346015453338623	1.8051	6	negative regulation of transcription		325
2.4306948675828823	2.1879	67	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		3075
2.43051519464044	2.0821	42	cellular component organization and biogenesis		2008
2.4235891212116587	2.3061	13	protein serine/threonine kinase activity	molecular function	544
2.420156256183163	2.5757	121	nucleus	cellular component	4692
2.416864479581515	2.3483	34	G-protein coupled receptor protein signaling pathway	biological process	1453
2.4153901100158692	2.0161	6	potassium ion transport		292
2.4113256633281708	4.7059	10	ice binding	molecular function	216
			response to freezing	biological process
			water binding	molecular function
	4.6784		homoiothermy	biological process	217
	4.4444		thermoregulation		226
2.410263843006558	2.0443	47	protein complex	cellular component	2308
2.4100664528933438	2.2358	13	protein-tyrosine kinase activity	molecular function	565
2.408202938131384	2.6038	89	biopolymer metabolic process	biological process	3425
2.403050871690114	3.0060	37	response to stress		1226
2.4005173126856487	2.0492	20	oxidoreductase activity	molecular function	955
2.3990859508514406	2.2422	6	soluble fraction	cellular component	256
2.3975469536251492	2.9801	10	positive regulation of transcription	biological process	338
	2.8939		positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		347
2.3974582254886627	3.4272	36	transcription factor activity	molecular function	1038
2.395317418234689	2.2307	46	cell surface receptor linked signal transduction	biological process	2077
2.3925783783197403	3.8095	9	enzyme linked receptor protein signaling pathway		230
2.3858967367693675	2.4996	181	cellular metabolic process		7233
2.383645436980508	2.1318	13	cellular lipid metabolic process		619
2.3829759624269276	2.1687	11	ion channel activity	molecular function	494
	2.0882		alpha-type channel activity		511
	2.0362		channel or pore class transporter activity		526
2.3798144817352296	3.2258	12	alcohol metabolic process	biological process	378
2.3753860882350377	2.3133	88	signal transduction		3816

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.