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

Results: HTML CSV LaTeX

Showing element 25 to 74 of 173 in total

Class  : biological process

Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	% Affected Genes	Class
2.6329536702897816	11	249	4.4554	response to temperature stimulus
2.630213709672292	42	1588	2.6362	transcription
2.6115847550905666	20	879	2.2184	immune system process
2.6086528982434953	9	318	2.9289	inflammatory response
2.5862315134568648	13	443	2.8646	ubiquitin cycle
2.5815784772237143	17	675	2.5554	protein amino acid phosphorylation
2.539123611790793	16	644	2.5045	organ development
2.5307046931523542	70	2985	2.3508	response to stimulus
2.530326783657074	12	416	2.8736	response to abiotic stimulus
2.5267262917298536	17	884	1.9118	DNA metabolic process
2.5005394551489086	21	1118	1.8711	cellular developmental process
2.4850547462701797	10	358	2.9197	response to wounding
2.4829982866843543	28	890	3.0968	phosphate metabolic process
				phosphorus metabolic process
2.470501118236118	52	1721	3.0405	protein modification process
		1780	2.9393	biopolymer modification
2.46775693159837	15	499	2.9680	regulation of transcription from RNA polymerase II promoter
2.453812837600708	11	552	1.9231	translation
2.4479837675352356	43	1442	2.9529	post-translational protein modification
2.4382004340489707	16	732	2.2514	sensory perception
		741	2.2181	neurological process
2.4346015453338623	6	325	1.8051	negative regulation of transcription
2.4306948675828823	67	3075	2.1879	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.43051519464044	42	2008	2.0821	cellular component organization and biogenesis
2.416864479581515	34	1453	2.3483	G-protein coupled receptor protein signaling pathway
2.4153901100158692	6	292	2.0161	potassium ion transport
2.4113256633281708	10	216	4.7059	response to freezing
		217	4.6784	homoiothermy
		226	4.4444	thermoregulation
2.408202938131384	89	3425	2.6038	biopolymer metabolic process
2.403050871690114	37	1226	3.0060	response to stress
2.3975469536251492	10	338	2.9801	positive regulation of transcription
		347	2.8939	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.395317418234689	46	2077	2.2307	cell surface receptor linked signal transduction
2.3925783783197403	9	230	3.8095	enzyme linked receptor protein signaling pathway
2.3858967367693675	181	7233	2.4996	cellular metabolic process
2.383645436980508	13	619	2.1318	cellular lipid metabolic process
2.3798144817352296	12	378	3.2258	alcohol metabolic process
2.3753860882350377	88	3816	2.3133	signal transduction
2.374769774137759	130	5408	2.4068	macromolecule metabolic process
2.3732517415826972	62	2448	2.5375	regulation of transcription, DNA-dependent
2.365392540051387	84	3325	2.5312	cellular protein metabolic process
		3377	2.4857	cellular macromolecule metabolic process
2.3636351216514155	208	8234	2.5270	metabolic process
2.3607054107329426	20	768	2.6235	protein transport
		810	2.4781	establishment of protein localization
2.357159194284982	178	7318	2.4343	primary metabolic process
2.329086923599243	6	107	5.1546	embryonic morphogenesis
2.328269682611738	90	3555	2.5307	protein metabolic process
2.319896697998047	13	534	2.5057	intracellular protein transport

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.