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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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