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 Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 173 in total

Class  : biological process

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class
9	3.4335	2.2164768129587173	264	organ morphogenesis
	2.9289	2.6086528982434953	318	inflammatory response
	2.5078	2.046714186668396	370	cell proliferation
	2.4922	2.8815125972032547	379	apoptosis
	2.4845		381	programmed cell death
	2.1390	2.1474349200725555	432	cell motility
	2.0202	2.1150057166814804	460	negative regulation of metabolic process
	1.6327	1.9312101155519485	570	carboxylic acid metabolic process
	1.6227		573	organic acid metabolic process
10	4.7059	2.4113256633281708	216	response to freezing
	4.6784		217	homoiothermy
	4.4444		226	thermoregulation
	2.9801	2.3975469536251492	338	positive regulation of transcription
	2.9197	2.4850547462701797	358	response to wounding
	2.8939	2.3975469536251492	347	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	2.5000	3.175950493131365	416	establishment and/or maintenance of chromatin architecture
	2.4561		422	DNA packaging
	2.2670	1.8413102626800537	448	RNA processing
	2.0349	3.175950493131365	496	chromosome organization and biogenesis (sensu Eukaryota)
	1.9824	2.121824940045675	510	vesicle-mediated transport
	1.9737	1.6538901064130995	527	regulation of cell proliferation
	1.8182	2.7119380235671997	531	cytoskeleton organization and biogenesis
	1.7699	1.7068785279989243	545	cellular biosynthetic process
11	5.0000	2.6329536702897816	226	response to cold
	4.4554		249	response to temperature stimulus
	2.6247	2.28793443441391	429	positive regulation of cellular metabolic process
	2.4658	2.8162122435039945	430	cell death
				death
	2.4631	2.28793443441391	456	positive regulation of metabolic process
	2.4272	2.0707096576690676	466	system development
	2.4064	2.6960288683573403	442	small GTPase mediated signal transduction
	2.1858	2.941256210207939	519	chromosome organization and biogenesis
	2.0179	2.123886121643914	534	regulation of apoptosis
	1.9912		540	regulation of programmed cell death
	1.9231	2.453812837600708	552	translation
	1.6701	1.9346576482057571	629	generation of precursor metabolites and energy
	1.5773	2.0859246611595155	727	cell differentiation
12	3.2258	2.3798144817352296	378	alcohol metabolic process
	2.8736	2.530326783657074	416	response to abiotic stimulus
	2.0661	2.1918027877807615	569	metal ion transport
13	2.8646	2.5862315134568648	443	ubiquitin cycle
	2.5172	1.6883443919095127	514	cell-cell signaling
	2.5057	2.319896697998047	534	intracellular protein transport
	2.1318	2.383645436980508	619	cellular lipid metabolic process
	2.0992	2.114047809080644	633	response to chemical stimulus
	2.0325	2.1211151123046874	663	macromolecular complex assembly
	1.9120		701	cellular component assembly
14	3.0303	1.6056334376335144	458	cell cycle
	2.2267	2.2604436332529243	634	response to external stimulus
	2.1164	2.105520764986674	669	cation transport

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.