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