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 173 in total

Class	biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	
3.175950493131365	2.5000	10	416	establishment and/or maintenance of chromatin architecture	
3.175950493131365	2.4561	10	422	DNA packaging	
3.175950493131365	2.0349	10	496	chromosome organization and biogenesis (sensu Eukaryota)	
3.0782742261886598	2.2026	15	680	defense response	
3.0316067695617677	2.7174	6	231	microtubule-based process	
2.9956377029418944	2.9412	6	195	chromatin modification	
2.941256210207939	2.1858	11	519	chromosome organization and biogenesis	
2.8815125972032547	2.4922	9	379	apoptosis	
2.8815125972032547	2.4845	9	381	programmed cell death	
2.844642996788025	2.9070	6	206	nucleocytoplasmic transport	
2.8162122435039945	2.4658	11	430	cell death	
2.8162122435039945	2.4658	11	430	death	
2.7829527854919434	2.8249	6	211	visual perception	
2.7829527854919434	2.8090	6	212	sensory perception of light stimulus	
2.7678764888218472	2.6820	33	1217	intracellular signaling cascade	
2.745920252799988	1.1390	6	544	carbohydrate metabolic process	
2.7119380235671997	1.8182	10	531	cytoskeleton organization and biogenesis	
2.6960288683573403	2.4064	11	442	small GTPase mediated signal transduction	
2.6894871592521667	5.7692	7	117	muscle development	
2.6829177481787547	3.9773	8	192	regulation of growth	
2.6820639967918396	2.6201	19	735	immune response	
2.644248050451279	2.1413	26	1204	organelle organization and biogenesis	
2.6417386531829834	2.5890	18	711	phosphorylation	
2.6329536702897816	5.0000	11	226	response to cold	
2.6329536702897816	4.4554	11	249	response to temperature stimulus	
2.630213709672292	2.6362	42	1588	transcription	
2.6115847550905666	2.2184	20	879	immune system process	
2.6086528982434953	2.9289	9	318	inflammatory response	
2.5862315134568648	2.8646	13	443	ubiquitin cycle	
2.5815784772237143	2.5554	17	675	protein amino acid phosphorylation	
2.539123611790793	2.5045	16	644	organ development	
2.5307046931523542	2.3508	70	2985	response to stimulus	
2.530326783657074	2.8736	12	416	response to abiotic stimulus	
2.5267262917298536	1.9118	17	884	DNA metabolic process	
2.5005394551489086	1.8711	21	1118	cellular developmental process	
2.4850547462701797	2.9197	10	358	response to wounding	
2.4829982866843543	3.0968	28	890	phosphate metabolic process	
2.4829982866843543	3.0968	28	890	phosphorus metabolic process	
2.470501118236118	3.0405	52	1721	protein modification process	
2.470501118236118	2.9393	52	1780	biopolymer modification	
2.46775693159837	2.9680	15	499	regulation of transcription from RNA polymerase II promoter	
2.453812837600708	1.9231	11	552	translation	
2.4479837675352356	2.9529	43	1442	post-translational protein modification	
2.4382004340489707	2.2514	16	732	sensory perception	
2.4382004340489707	2.2181	16	741	neurological process	
2.4346015453338623	1.8051	6	325	negative regulation of transcription	
2.4306948675828823	2.1879	67	3075	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	
2.43051519464044	2.0821	42	2008	cellular component organization and biogenesis	
2.416864479581515	2.3483	34	1453	G-protein coupled receptor protein signaling pathway	
2.4153901100158692	2.0161	6	292	potassium ion transport	

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/