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	Class	affected	Microarray Measured (#genes)	Accession	Class Size (#genes)

Results: HTML CSV LaTeX

Showing element 1 to 50 of 328 in total

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