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