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