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