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	Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#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	Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#genes)	Class
2.2856	120	2.0664001241807015	5267	biological regulation
2.2670	10	1.8413102626800537	448	RNA processing
2.2514	16	2.4382004340489707	732	sensory perception
2.2398	20	2.1725611826952766	914	establishment of cellular localization
2.2364	17	2.2737072706222534	752	lipid metabolic process
2.2321	6	1.368695902824402	260	chemical homeostasis
2.2307	46	2.395317418234689	2077	cell surface receptor linked signal transduction
2.2267	14	2.2604436332529243	634	response to external stimulus
2.2184	20	2.6115847550905666	879	immune system process
2.2181	16	2.4382004340489707	741	neurological process
2.2167	22	2.02202084991667	974	ion transport
2.2026	15	3.0782742261886598	680	defense response
2.1930	6	1.8477724552154542	287	cell-cell adhesion
2.1879	67	2.4306948675828823	3075	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.1858	11	2.941256210207939	519	chromosome organization and biogenesis
2.1417	17	1.9759902954101562	800	proteolysis
2.1413	26	2.644248050451279	1204	organelle organization and biogenesis
2.1407	17	1.8383450422968184	806	biological adhesion
				cell adhesion
2.1390	9	2.1474349200725555	432	cell motility
2.1368	6	1.7971266508102417	275	lipid biosynthetic process
2.1318	13	2.383645436980508	619	cellular lipid metabolic process
2.1164	14	2.105520764986674	669	cation transport
2.0992	13	2.114047809080644	633	response to chemical stimulus
2.0945	48	1.9769652134332902	2294	multicellular organismal process
2.0833	7	1.9949067831039429	335	protein complex assembly
2.0821	42	2.43051519464044	2008	cellular component organization and biogenesis
2.0661	6	1.9144784212112427	272	positive regulation of cell proliferation
	12	2.1918027877807615	569	metal ion transport
2.0492	6	1.3052469968795777	276	regulation of developmental process
2.0349	10	3.175950493131365	496	chromosome organization and biogenesis (sensu Eukaryota)
2.0325	13	2.1211151123046874	663	macromolecular complex assembly
	17	1.714063827196757	851	multicellular organismal development
2.0202	7	1.6523104111353557	337	response to DNA damage stimulus
	9	2.1150057166814804	460	negative regulation of metabolic process
	15	2.243723976612091	762	macromolecule biosynthetic process
	17	2.16537378515516	840	intracellular transport
2.0179	11	2.123886121643914	534	regulation of apoptosis
2.0161	6	2.4153901100158692	292	potassium ion transport
	23	2.2058627247810363	1164	negative regulation of cellular process
1.9912	11	2.123886121643914	540	regulation of programmed cell death
1.9841	6	1.7531960964202882	289	mRNA metabolic process
1.9824	10	2.121824940045675	510	vesicle-mediated transport
1.9737		1.6538901064130995	527	regulation of cell proliferation
1.9608	7	2.2540424267450967	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	8	2.2326475211552212	414	negative regulation of cellular metabolic process
1.9231	11	2.453812837600708	552	translation
1.9204	16	2.0980815972600664	832	RNA metabolic process
1.9120	13	2.1211151123046874	701	cellular component assembly
1.9118	17	2.5267262917298536	884	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.