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	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 101 to 150 of 173 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)	Class
2.2856	2.0664001241807015	5267	120	biological regulation
2.2670	1.8413102626800537	448	10	RNA processing
2.2514	2.4382004340489707	732	16	sensory perception
2.2398	2.1725611826952766	914	20	establishment of cellular localization
2.2364	2.2737072706222534	752	17	lipid metabolic process
2.2321	1.368695902824402	260	6	chemical homeostasis
2.2307	2.395317418234689	2077	46	cell surface receptor linked signal transduction
2.2267	2.2604436332529243	634	14	response to external stimulus
2.2184	2.6115847550905666	879	20	immune system process
2.2181	2.4382004340489707	741	16	neurological process
2.2167	2.02202084991667	974	22	ion transport
2.2026	3.0782742261886598	680	15	defense response
2.1930	1.8477724552154542	287	6	cell-cell adhesion
2.1879	2.4306948675828823	3075	67	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.1858	2.941256210207939	519	11	chromosome organization and biogenesis
2.1417	1.9759902954101562	800	17	proteolysis
2.1413	2.644248050451279	1204	26	organelle organization and biogenesis
2.1407	1.8383450422968184	806	17	biological adhesion
				cell adhesion
2.1390	2.1474349200725555	432	9	cell motility
2.1368	1.7971266508102417	275	6	lipid biosynthetic process
2.1318	2.383645436980508	619	13	cellular lipid metabolic process
2.1164	2.105520764986674	669	14	cation transport
2.0992	2.114047809080644	633	13	response to chemical stimulus
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

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.