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 Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Microarray Measured (#genes)	Average Regulation (ratio)	affected	Class	Accession

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Average Regulation (ratio)
6.3492	9	protein amino acid dephosphorylation	142	2.1655175536870956
5.7692	7	muscle development	117	2.6894871592521667
5.7143	9	dephosphorylation	158	2.1655175536870956
5.1546	6	embryonic morphogenesis	107	2.329086923599243
5.0000	11	response to cold	226	2.6329536702897816
4.7244	7	mitosis	142	1.632481078306834
4.7059	10	response to freezing	216	2.4113256633281708
4.6784		homoiothermy	217
4.4554	11	response to temperature stimulus	249	2.6329536702897816
4.4444	10	thermoregulation	226	2.4113256633281708
4.3573	23	regulation of progression through cell cycle	535	1.8484420895576477
4.3197		regulation of cell cycle	539
3.9773	8	regulation of growth	192	2.6829177481787547
3.9735	7	transmembrane receptor protein tyrosine kinase signaling pathway	164	2.267966568470001
3.8095	9	enzyme linked receptor protein signaling pathway	230	2.3925783783197403
3.7234	8	RNA splicing	208	1.8230999537876673
3.5604	27	cell cycle process	746	1.8924930147502734
3.4335	9	organ morphogenesis	264	2.2164768129587173
3.4146	8	cell cycle phase	229	1.6467143297195435
3.3333	6	regulation of cell differentiation	170	1.3052469968795777
3.2258	12	alcohol metabolic process	378	2.3798144817352296
3.0968	28	phosphate metabolic process	890	2.4829982866843543
		phosphorus metabolic process
3.0405	52	protein modification process	1721	2.470501118236118
3.0303	7	cell division	222	1.3425244291623433
	14	cell cycle	458	1.6056334376335144
3.0060	37	response to stress	1226	2.403050871690114
2.9801	10	positive regulation of transcription	338	2.3975469536251492
2.9680	15	regulation of transcription from RNA polymerase II promoter	499	2.46775693159837
2.9529	43	post-translational protein modification	1442	2.4479837675352356
2.9412	6	chromatin modification	195	2.9956377029418944
2.9393	52	biopolymer modification	1780	2.470501118236118
2.9289	9	inflammatory response	318	2.6086528982434953
2.9197	10	response to wounding	358	2.4850547462701797
2.9070	6	nucleocytoplasmic transport	206	2.844642996788025
2.8939	10	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	347	2.3975469536251492
2.8736	12	response to abiotic stimulus	416	2.530326783657074
2.8646	13	ubiquitin cycle	443	2.5862315134568648
2.8333	19	anatomical structure morphogenesis	686	2.1418599311043236
2.8249	6	visual perception	211	2.7829527854919434
2.8090		sensory perception of light stimulus	212
2.7174		microtubule-based process	231	3.0316067695617677
2.6820	33	intracellular signaling cascade	1217	2.7678764888218472
2.6596	6	anion transport	229	1.6556044340133667
2.6362	42	transcription	1588	2.630213709672292
2.6247	11	positive regulation of cellular metabolic process	429	2.28793443441391
2.6245	69	regulation of transcription	2628	2.3178554457061145
2.6235	20	protein transport	768	2.3607054107329426
2.6201	19	immune response	735	2.6820639967918396
2.6103	33	anatomical structure development	1273	2.1811264465595115

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.