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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Class	Would Be Affected (#genes)	Class
2.3310728073120117	33.3333	3	cellular component	1	cullin-RING ubiquitin ligase complex
					SCF ubiquitin ligase complex
2.329086923599243	5.1546	107	biological process	6	embryonic morphogenesis
2.328269682611738	2.5307	3555		90	protein metabolic process
2.319896697998047	2.5057	534		13	intracellular protein transport
2.31939160823822	3.3898	67	cellular component	2	contractile fiber part
2.3178554457061145	2.6245	2628	biological process	69	regulation of transcription
2.317225064550127	1.7677	510	cellular component	9	extracellular space
2.316990613937378	33.3333	5	molecular function	2	protein phosphatase type 2A activity
	5.2632	21	cellular component	1	protein phosphatase type 2A complex
2.3127479553222656	1.4970	398	biological process	6	behavior
2.312502180275164	2.3114	4136		96	cell communication
2.3103933334350586	25.0000	5		1	maintenance of protein localization in nucleus
	4.7619	25			maintenance of cellular protein localization
		26			maintenance of protein localization
	4.3478	27			maintenance of cellular localization
	3.5714	34			maintenance of localization
2.309741258621216	3.0534	168	cellular component	5	microsome
	2.9412	173			vesicular fraction
2.3059755516052247	2.2085	2892		64	intracellular organelle part
	2.2017	2900			organelle part
2.3038527108075324	2.4081	2739	biological process	66	developmental process
2.3028621958649675	2.4798	2641	molecular function	65	DNA binding
2.299432896077633	1.8561	1060	cellular component	20	integral to plasma membrane
	1.8286	1077			intrinsic to plasma membrane
2.2985232734680174	2.5907	2698	biological process	70	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.293897867202759	3.5714	33		1	pigmentation
2.2892844676971436	5.3571	59	molecular function	3	protein C-terminus binding
2.2890394926071167	11.1111	21	biological process	2	peptide metabolic process
2.28793443441391	2.6247	429		11	positive regulation of cellular metabolic process
	2.4631	456			positive regulation of metabolic process
2.28659725189209	6.2500	18	molecular function	1	protein phosphatase type 2C activity
2.2792132452352725	2.5000	3858		96	nucleic acid binding
2.27594193816185	3.8462	124	biological process	5	protein amino acid glycosylation
	3.7736	126			biopolymer glycosylation
2.2737072706222534	2.2364	752		17	lipid metabolic process
2.2681225514251913	2.4354	7366	molecular function	179	protein binding
2.267966568470001	3.9735	164	biological process	7	transmembrane receptor protein tyrosine kinase signaling pathway
2.2671763740532787	2.3725	15762	cellular component	374	cellular_component
2.2670372059712043	2.4610	2913	biological process	72	regulation of cellular metabolic process
2.2664323395275208	2.4356	18539	universal	452	all
2.266423319776853	2.9091	972	cellular component	28	cell fraction
2.2657248179117837	1.3100	281		4	proteinaceous extracellular matrix
2.2609615601026096	2.4030	734	molecular function	18	peptidase activity
2.2604436332529243	2.2267	634	biological process	14	response to external stimulus
2.2601398825645447	1.5228	464		7	monovalent inorganic cation transport
2.259546995162964	33.3333	3		1	threonyl-tRNA aminoacylation
			molecular function		threonine-tRNA ligase activity
	1.3889	79	biological process		amino acid activation
					tRNA aminoacylation

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.