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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Would Be Affected (#genes)	Class	Class
3.243556241194407	5.4545	118	6	molecular function	potassium ion binding
	3.4682	191	7		alkali metal ion binding
3.175950493131365	2.5000	416	10	biological process	establishment and/or maintenance of chromatin architecture
	2.4561	422			DNA packaging
	2.0349	496			chromosome organization and biogenesis (sensu Eukaryota)
3.0782742261886598	2.2026	680	15		defense response
3.0316067695617677	2.7174	231	6		microtubule-based process
2.9956377029418944	2.9412	195			chromatin modification
2.9851186752319334	1.3369	448		molecular function	lipid binding
2.9601402282714844	4.8000	184	9	cellular component	chromatin
2.941256210207939	2.1858	519	11	biological process	chromosome organization and biogenesis
2.9320233133104114	1.9459	1086	21	molecular function	transferase activity, transferring phosphorus-containing groups
2.8815125972032547	2.4922	379	9	biological process	apoptosis
	2.4845	381			programmed cell death
2.844642996788025	2.9070	206	6		nucleocytoplasmic transport
2.8238616314801304	3.4700	472	16	cellular component	chromosomal part
2.8162122435039945	2.4658	430	11	biological process	cell death
					death
2.8144334629178047	2.3088	810	19	molecular function	phosphotransferase activity, alcohol group as acceptor
2.7959404488404593	4.0268	360	14		protein dimerization activity
2.7829527854919434	2.8249	211	6	biological process	visual perception
	2.8090	212			sensory perception of light stimulus
2.7678764888218472	2.6820	1217	33		intracellular signaling cascade
2.745920252799988	1.1390	544	6		carbohydrate metabolic process
2.718373046201818	2.1277	938	20	molecular function	kinase activity
2.7119380235671997	1.8182	531	10	biological process	cytoskeleton organization and biogenesis
2.7082830667495728	1.7921	636	11	cellular component	cytoskeleton
2.6960288683573403	2.4064	442		biological process	small GTPase mediated signal transduction
2.6934666122709	2.1605	379	8	cellular component	nucleoplasm part
2.6894871592521667	5.7692	117	7	biological process	muscle development
2.6829177481787547	3.9773	192	8		regulation of growth
2.6820639967918396	2.6201	735	19		immune response
2.6707380056381225	2.3502	990	23	cellular component	nuclear part
2.659621460097177	1.7926	1890	34	molecular function	transferase activity
2.644248050451279	2.1413	1204	26	biological process	organelle organization and biogenesis
2.6417386531829834	2.5890	711	18		phosphorylation
2.6377359429995217	2.2556	315	7	molecular function	voltage-gated ion channel activity
2.6329536702897816	5.0000	226	11	biological process	response to cold
	4.4554	249			response to temperature stimulus
2.630213709672292	2.6362	1588	42		transcription
2.6115847550905666	2.2184	879	20		immune system process
2.6086528982434953	2.9289	318	9		inflammatory response
2.599970555305481	3.5971	182	7	molecular function	amine receptor activity
2.5862315134568648	2.8646	443	13	biological process	ubiquitin cycle
2.5815784772237143	2.5554	675	17		protein amino acid phosphorylation
2.5402226646741233	3.6145	245	9	cellular component	chromosome
2.539123611790793	2.5045	644	16	biological process	organ development
2.5307046931523542	2.3508	2985	70		response to stimulus
2.530326783657074	2.8736	416	12		response to abiotic stimulus
2.5267262917298536	1.9118	884	17		DNA metabolic process

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.