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