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

Results: HTML CSV LaTeX

Showing element 175 to 224 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Would Be Affected (#genes)	Class
2.6354507505893707	1.9900	229	5	RNA biosynthetic process
2.6329536702897816	5.0000	226	11	response to cold
	4.4554	249		response to temperature stimulus
2.630213709672292	2.6362	1588	42	transcription
2.614621639251709	2.4194	137	3	carboxylic acid transport
		138		organic acid transport
2.6115847550905666	2.2184	879	20	immune system process
2.611353635787964	25.0000	4	1	peptide biosynthetic process
	20.0000	5		DNA damage response, detection of DNA damage
2.6086528982434953	2.9289	318	9	inflammatory response
2.5862315134568648	2.8646	443	13	ubiquitin cycle
2.5815784772237143	2.5554	675	17	protein amino acid phosphorylation
2.5450799465179443	33.3333	3	1	intercellular junction maintenance
	5.8824	18		intercellular junction assembly and maintenance
	4.3478	25		cytoplasm organization and biogenesis
2.539123611790793	2.5045	644	16	organ development
2.531393676996231	2.2599	210	5	membrane lipid metabolic process
2.5307046931523542	2.3508	2985	70	response to stimulus
2.530326783657074	2.8736	416	12	response to abiotic stimulus
2.5267262917298536	1.9118	884	17	DNA metabolic process
2.524488886197408	1.4493	235	3	monocarboxylic acid metabolic process
2.5005394551489086	1.8711	1118	21	cellular developmental process
2.4850547462701797	2.9197	358	10	response to wounding
2.4845048983891806	1.0714	349	4	cellular macromolecule catabolic process
2.4829982866843543	3.0968	890	28	phosphate metabolic process
				phosphorus metabolic process
2.4747204780578613	8.1633	61	5	regulation of mitosis
2.470501118236118	3.0405	1721	52	protein modification process
	2.9393	1780		biopolymer modification
2.46775693159837	2.9680	499	15	regulation of transcription from RNA polymerase II promoter
2.45763897895813	6.2500	19	1	zinc ion transport
2.453812837600708	1.9231	552	11	translation
2.4495278000831604	6.6667	41	3	regulation of neuron apoptosis
2.4479837675352356	2.9529	1442	43	post-translational protein modification
2.4382004340489707	2.2514	732	16	sensory perception
	2.2181	741		neurological process
2.4365404844284058	12.5000	32	4	translational elongation
	3.7037	75	3	biopolymer biosynthetic process
2.4346015453338623	1.8051	325	6	negative regulation of transcription
2.430976390838623	1.3889	97	1	lipid transport
2.4306948675828823	2.1879	3075	67	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.43051519464044	2.0821	2008	42	cellular component organization and biogenesis
2.416864479581515	2.3483	1453	34	G-protein coupled receptor protein signaling pathway
2.4153901100158692	2.0161	292	6	potassium ion transport
2.4113256633281708	4.7059	216	10	response to freezing
	4.6784	217		homoiothermy
	4.4444	226		thermoregulation
2.408202938131384	2.6038	3425	89	biopolymer metabolic process
2.403050871690114	3.0060	1226	37	response to stress
2.3975469536251492	2.9801	338	10	positive regulation of transcription

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.