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	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

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