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