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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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