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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)
3.175950493131365	2.5000	10	establishment and/or maintenance of chromatin architecture	416
	2.4561		DNA packaging	422
	2.0349		chromosome organization and biogenesis (sensu Eukaryota)	496
3.0782742261886598	2.2026	15	defense response	680
3.0316067695617677	2.7174	6	microtubule-based process	231
2.9956377029418944	2.9412		chromatin modification	195
2.941256210207939	2.1858	11	chromosome organization and biogenesis	519
2.8815125972032547	2.4922	9	apoptosis	379
	2.4845		programmed cell death	381
2.844642996788025	2.9070	6	nucleocytoplasmic transport	206
2.8162122435039945	2.4658	11	cell death	430
			death
2.7829527854919434	2.8249	6	visual perception	211
	2.8090		sensory perception of light stimulus	212
2.7678764888218472	2.6820	33	intracellular signaling cascade	1217
2.745920252799988	1.1390	6	carbohydrate metabolic process	544
2.7119380235671997	1.8182	10	cytoskeleton organization and biogenesis	531
2.6960288683573403	2.4064	11	small GTPase mediated signal transduction	442
2.6894871592521667	5.7692	7	muscle development	117
2.6829177481787547	3.9773	8	regulation of growth	192
2.6820639967918396	2.6201	19	immune response	735
2.644248050451279	2.1413	26	organelle organization and biogenesis	1204
2.6417386531829834	2.5890	18	phosphorylation	711
2.6329536702897816	5.0000	11	response to cold	226
	4.4554		response to temperature stimulus	249
2.630213709672292	2.6362	42	transcription	1588
2.6115847550905666	2.2184	20	immune system process	879
2.6086528982434953	2.9289	9	inflammatory response	318
2.5862315134568648	2.8646	13	ubiquitin cycle	443
2.5815784772237143	2.5554	17	protein amino acid phosphorylation	675
2.539123611790793	2.5045	16	organ development	644
2.5307046931523542	2.3508	70	response to stimulus	2985
2.530326783657074	2.8736	12	response to abiotic stimulus	416
2.5267262917298536	1.9118	17	DNA metabolic process	884
2.5005394551489086	1.8711	21	cellular developmental process	1118
2.4850547462701797	2.9197	10	response to wounding	358
2.4829982866843543	3.0968	28	phosphate metabolic process	890
			phosphorus metabolic process
2.470501118236118	3.0405	52	protein modification process	1721
	2.9393		biopolymer modification	1780
2.46775693159837	2.9680	15	regulation of transcription from RNA polymerase II promoter	499
2.453812837600708	1.9231	11	translation	552
2.4479837675352356	2.9529	43	post-translational protein modification	1442
2.4382004340489707	2.2514	16	sensory perception	732
	2.2181		neurological process	741
2.4346015453338623	1.8051	6	negative regulation of transcription	325
2.4306948675828823	2.1879	67	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	3075
2.43051519464044	2.0821	42	cellular component organization and biogenesis	2008
2.416864479581515	2.3483	34	G-protein coupled receptor protein signaling pathway	1453
2.4153901100158692	2.0161	6	potassium ion transport	292

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.