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 [...,...].

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class	Class	Class Size (#genes)	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 173 in total

Class  : biological process

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class	Class Size (#genes)
11	4.4554	2.6329536702897816	response to temperature stimulus	249
	2.6247	2.28793443441391	positive regulation of cellular metabolic process	429
	2.4658	2.8162122435039945	cell death	430
			death
	2.4631	2.28793443441391	positive regulation of metabolic process	456
	2.4272	2.0707096576690676	system development	466
	2.4064	2.6960288683573403	small GTPase mediated signal transduction	442
	2.1858	2.941256210207939	chromosome organization and biogenesis	519
	2.0179	2.123886121643914	regulation of apoptosis	534
	1.9912		regulation of programmed cell death	540
	1.9231	2.453812837600708	translation	552
	1.6701	1.9346576482057571	generation of precursor metabolites and energy	629
	1.5773	2.0859246611595155	cell differentiation	727
12	3.2258	2.3798144817352296	alcohol metabolic process	378
	2.8736	2.530326783657074	response to abiotic stimulus	416
	2.0661	2.1918027877807615	metal ion transport	569
13	2.8646	2.5862315134568648	ubiquitin cycle	443
	2.5172	1.6883443919095127	cell-cell signaling	514
	2.5057	2.319896697998047	intracellular protein transport	534
	2.1318	2.383645436980508	cellular lipid metabolic process	619
	2.0992	2.114047809080644	response to chemical stimulus	633
	2.0325	2.1211151123046874	macromolecular complex assembly	663
	1.9120		cellular component assembly	701
14	3.0303	1.6056334376335144	cell cycle	458
	2.2267	2.2604436332529243	response to external stimulus	634
	2.1164	2.105520764986674	cation transport	669
15	2.9680	2.46775693159837	regulation of transcription from RNA polymerase II promoter	499
	2.2026	3.0782742261886598	defense response	680
	2.0202	2.243723976612091	macromolecule biosynthetic process	762
16	2.5048	2.0103142169805674	homeostatic process	623
	2.5045	2.539123611790793	organ development	644
	2.3679	2.0103142169805674	regulation of biological quality	660
	2.2514	2.4382004340489707	sensory perception	732
	2.2181		neurological process	741
	1.9204	2.0980815972600664	RNA metabolic process	832
17	2.5554	2.5815784772237143	protein amino acid phosphorylation	675
	2.2364	2.2737072706222534	lipid metabolic process	752
	2.1417	1.9759902954101562	proteolysis	800
	2.1407	1.8383450422968184	biological adhesion	806
			cell adhesion
	2.0325	1.714063827196757	multicellular organismal development	851
	2.0202	2.16537378515516	intracellular transport	840
	1.9118	2.5267262917298536	DNA metabolic process	884
18	2.5890	2.6417386531829834	phosphorylation	711
19	2.8333	2.1418599311043236	anatomical structure morphogenesis	686
	2.6201	2.6820639967918396	immune response	735
20	2.6235	2.3607054107329426	protein transport	768
	2.4781		establishment of protein localization	810
	2.2398	2.1725611826952766	establishment of cellular localization	914
	2.2184	2.6115847550905666	immune system process	879

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.