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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

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

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.