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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

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

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.