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

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.