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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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