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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)	Class
2.0945	1.9769652134332902	2294	48	multicellular organismal process
2.0833	1.9949067831039429	335	7	protein complex assembly
2.0821	2.43051519464044	2008	42	cellular component organization and biogenesis
2.0661	2.1918027877807615	569	12	metal ion transport
	1.9144784212112427	272	6	positive regulation of cell proliferation
2.0492	1.3052469968795777	276		regulation of developmental process
2.0349	3.175950493131365	496	10	chromosome organization and biogenesis (sensu Eukaryota)
2.0325	2.1211151123046874	663	13	macromolecular complex assembly
	1.714063827196757	851	17	multicellular organismal development
2.0202	2.243723976612091	762	15	macromolecule biosynthetic process
	2.16537378515516	840	17	intracellular transport
	2.1150057166814804	460	9	negative regulation of metabolic process
	1.6523104111353557	337	7	response to DNA damage stimulus
2.0179	2.123886121643914	534	11	regulation of apoptosis
2.0161	2.4153901100158692	292	6	potassium ion transport
	2.2058627247810363	1164	23	negative regulation of cellular process
1.9912	2.123886121643914	540	11	regulation of programmed cell death
1.9841	1.7531960964202882	289	6	mRNA metabolic process
1.9824	2.121824940045675	510	10	vesicle-mediated transport
1.9737	1.6538901064130995	527		regulation of cell proliferation
1.9608	2.2540424267450967	358	7	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	2.2326475211552212	414	8	negative regulation of cellular metabolic process
1.9231	2.453812837600708	552	11	translation
1.9204	2.0980815972600664	832	16	RNA metabolic process
1.9120	2.1211151123046874	701	13	cellular component assembly
1.9118	2.5267262917298536	884	17	DNA metabolic process
1.8957	2.2058627247810363	1238	23	negative regulation of biological process
1.8727	1.575242853164673	314	6	amino acid metabolic process
1.8711	2.5005394551489086	1118	21	cellular developmental process
1.8421	2.158773183822632	428	8	response to endogenous stimulus
1.8357	1.9786490954850848	1417	26	biosynthetic process
1.8293	1.5113894144694011	388	7	amino acid and derivative metabolic process
1.8182	2.7119380235671997	531	10	cytoskeleton organization and biogenesis
1.8051	2.4346015453338623	325	6	negative regulation of transcription
1.7949	1.5929162161690849	463	8	amine metabolic process
1.7699	1.7068785279989243	545	10	cellular biosynthetic process
1.7157	1.5929162161690849	484	8	nitrogen compound metabolic process
1.6701	1.9346576482057571	629	11	generation of precursor metabolites and energy
1.6327	1.9312101155519485	570	9	carboxylic acid metabolic process
1.6227		573		organic acid metabolic process
1.6092	1.6290612050465174	527	8	regulation of a molecular function
1.5773	2.0859246611595155	727	11	cell differentiation
1.5748	1.4910563230514526	514	8	electron transport
1.5228	2.2601398825645447	464	7	monovalent inorganic cation transport
1.4970	2.3127479553222656	398	6	behavior
1.4634	1.683560033639272	501	7	regulation of catalytic activity
1.1390	2.745920252799988	544	6	carbohydrate metabolic process
1.0870	1.9687834978103638	559		cellular catabolic process
0.8741		704		catabolic 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.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.