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