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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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