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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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

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.