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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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

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.