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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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