Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

- http://analysis.yellowcouch.org/