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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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