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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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

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.