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	Would Be Affected (#genes)	Class	Class Size (#genes)	affected	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 451 to 500 of 8866 in total

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