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