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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class	Class Size (#genes)	Would Be Affected (#genes)
3.175950493131365	2.5000	establishment and/or maintenance of chromatin architecture	416	10
	2.4561	DNA packaging	422
	2.0349	chromosome organization and biogenesis (sensu Eukaryota)	496
3.0782742261886598	2.2026	defense response	680	15
3.0316067695617677	2.7174	microtubule-based process	231	6
2.9956377029418944	2.9412	chromatin modification	195
2.941256210207939	2.1858	chromosome organization and biogenesis	519	11
2.8815125972032547	2.4922	apoptosis	379	9
	2.4845	programmed cell death	381
2.844642996788025	2.9070	nucleocytoplasmic transport	206	6
2.8162122435039945	2.4658	cell death	430	11
		death
2.7829527854919434	2.8249	visual perception	211	6
	2.8090	sensory perception of light stimulus	212
2.7678764888218472	2.6820	intracellular signaling cascade	1217	33
2.745920252799988	1.1390	carbohydrate metabolic process	544	6
2.7119380235671997	1.8182	cytoskeleton organization and biogenesis	531	10
2.6960288683573403	2.4064	small GTPase mediated signal transduction	442	11
2.6894871592521667	5.7692	muscle development	117	7
2.6829177481787547	3.9773	regulation of growth	192	8
2.6820639967918396	2.6201	immune response	735	19
2.644248050451279	2.1413	organelle organization and biogenesis	1204	26
2.6417386531829834	2.5890	phosphorylation	711	18
2.6329536702897816	5.0000	response to cold	226	11
	4.4554	response to temperature stimulus	249
2.630213709672292	2.6362	transcription	1588	42
2.6115847550905666	2.2184	immune system process	879	20
2.6086528982434953	2.9289	inflammatory response	318	9
2.5862315134568648	2.8646	ubiquitin cycle	443	13
2.5815784772237143	2.5554	protein amino acid phosphorylation	675	17
2.539123611790793	2.5045	organ development	644	16
2.5307046931523542	2.3508	response to stimulus	2985	70
2.530326783657074	2.8736	response to abiotic stimulus	416	12
2.5267262917298536	1.9118	DNA metabolic process	884	17
2.5005394551489086	1.8711	cellular developmental process	1118	21
2.4850547462701797	2.9197	response to wounding	358	10
2.4829982866843543	3.0968	phosphate metabolic process	890	28
		phosphorus metabolic process
2.470501118236118	3.0405	protein modification process	1721	52
	2.9393	biopolymer modification	1780
2.46775693159837	2.9680	regulation of transcription from RNA polymerase II promoter	499	15
2.453812837600708	1.9231	translation	552	11
2.4479837675352356	2.9529	post-translational protein modification	1442	43
2.4382004340489707	2.2514	sensory perception	732	16
	2.2181	neurological process	741
2.4346015453338623	1.8051	negative regulation of transcription	325	6
2.4306948675828823	2.1879	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	3075	67
2.43051519464044	2.0821	cellular component organization and biogenesis	2008	42
2.416864479581515	2.3483	G-protein coupled receptor protein signaling pathway	1453	34
2.4153901100158692	2.0161	potassium ion transport	292	6

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.