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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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