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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class	Class
3.243556241194407	6	5.4545	118	molecular function	potassium ion binding
	7	3.4682	191		alkali metal ion binding
3.175950493131365	10	2.5000	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	15	2.2026	680		defense response
3.0316067695617677	6	2.7174	231		microtubule-based process
2.9956377029418944		2.9412	195		chromatin modification
2.9851186752319334		1.3369	448	molecular function	lipid binding
2.9601402282714844	9	4.8000	184	cellular component	chromatin
2.941256210207939	11	2.1858	519	biological process	chromosome organization and biogenesis
2.9320233133104114	21	1.9459	1086	molecular function	transferase activity, transferring phosphorus-containing groups
2.8815125972032547	9	2.4922	379	biological process	apoptosis
		2.4845	381		programmed cell death
2.844642996788025	6	2.9070	206		nucleocytoplasmic transport
2.8238616314801304	16	3.4700	472	cellular component	chromosomal part
2.8162122435039945	11	2.4658	430	biological process	cell death
					death
2.8144334629178047	19	2.3088	810	molecular function	phosphotransferase activity, alcohol group as acceptor
2.7959404488404593	14	4.0268	360		protein dimerization activity
2.7829527854919434	6	2.8249	211	biological process	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
2.718373046201818	20	2.1277	938	molecular function	kinase activity
2.7119380235671997	10	1.8182	531	biological process	cytoskeleton organization and biogenesis
2.7082830667495728	11	1.7921	636	cellular component	cytoskeleton
2.6960288683573403		2.4064	442	biological process	small GTPase mediated signal transduction
2.6934666122709	8	2.1605	379	cellular component	nucleoplasm part
2.6894871592521667	7	5.7692	117	biological process	muscle development
2.6829177481787547	8	3.9773	192		regulation of growth
2.6820639967918396	19	2.6201	735		immune response
2.6707380056381225	23	2.3502	990	cellular component	nuclear part
2.659621460097177	34	1.7926	1890	molecular function	transferase activity
2.644248050451279	26	2.1413	1204	biological process	organelle organization and biogenesis
2.6417386531829834	18	2.5890	711		phosphorylation
2.6377359429995217	7	2.2556	315	molecular function	voltage-gated ion channel activity
2.6329536702897816	11	5.0000	226	biological process	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
2.599970555305481	7	3.5971	182	molecular function	amine receptor activity
2.5862315134568648	13	2.8646	443	biological process	ubiquitin cycle
2.5815784772237143	17	2.5554	675		protein amino acid phosphorylation
2.5402226646741233	9	3.6145	245	cellular component	chromosome
2.539123611790793	16	2.5045	644	biological process	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

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.