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