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