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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)	Class
2.3127479553222656	1.4970	behavior	6	398	biological process
2.312502180275164	2.3114	cell communication	96	4136
2.3059755516052247	2.2085	intracellular organelle part	64	2892	cellular component
	2.2017	organelle part		2900
2.3038527108075324	2.4081	developmental process	66	2739	biological process
2.3028621958649675	2.4798	DNA binding	65	2641	molecular function
2.299432896077633	1.8561	integral to plasma membrane	20	1060	cellular component
	1.8286	intrinsic to plasma membrane		1077
2.2985232734680174	2.5907	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	70	2698	biological process
2.28793443441391	2.6247	positive regulation of cellular metabolic process	11	429
	2.4631	positive regulation of metabolic process		456
2.2792132452352725	2.5000	nucleic acid binding	96	3858	molecular function
2.2737072706222534	2.2364	lipid metabolic process	17	752	biological process
2.2681225514251913	2.4354	protein binding	179	7366	molecular function
2.267966568470001	3.9735	transmembrane receptor protein tyrosine kinase signaling pathway	7	164	biological process
2.2671763740532787	2.3725	cellular_component	374	15762	cellular component
2.2670372059712043	2.4610	regulation of cellular metabolic process	72	2913	biological process
2.2664323395275208	2.4356	all	452	18539	universal
2.266423319776853	2.9091	cell fraction	28	972	cellular component
2.2609615601026096	2.4030	peptidase activity	18	734	molecular function
2.2604436332529243	2.2267	response to external stimulus	14	634	biological process
2.2601398825645447	1.5228	monovalent inorganic cation transport	7	464
2.259431820927244	2.3913	molecular_function	401	16757	molecular function
2.2576280551010304	2.3831	cell part	352	14761	cellular component
2.2540424267450967	1.9608	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	7	358	biological process
2.252760338363143	2.4522	cellular process	294	11986
2.248631090488074	2.4047	regulation of metabolic process	73	3018
2.246480769722174	2.4413	biological_process	377	15431
2.243723976612091	2.0202	macromolecule biosynthetic process	15	762
2.241470267334763	2.4400	binding	319	13082	molecular function
2.2348088707242693	2.5271	nervous system development	8	321	biological process
2.2326475211552212	1.9608	negative regulation of cellular metabolic process		414
2.231512101073014	3.0400	membrane fraction	22	739	cellular component
2.2257004976272583	1.8248	olfactory receptor activity	9	497	molecular function
2.2204760638150303	1.6923	extracellular region part	14	826	cellular component
2.220401409599516	2.2099	zinc ion binding	53	2403	molecular function
2.216642654982189	2.4279	intracellular organelle	192	7902	cellular component
	2.4275	organelle		7904
2.2164768129587173	3.4335	organ morphogenesis	9	264	biological process
2.215940025315356	2.4157	intracellular membrane-bound organelle	170	7030	cellular component
		membrane-bound organelle
2.210925724557651	2.3834	intracellular part	239	10046
2.2093183655257618	2.3335	catalytic activity	137	5858	molecular function
2.2058627247810363	2.0161	negative regulation of cellular process	23	1164	biological process
	1.8957	negative regulation of biological process		1238
2.201751559972763	1.8244	G-protein coupled receptor activity		1284	molecular function
2.201178240776062	3.3727	hydrolase activity, acting on ester bonds	24	723
2.195966625213623	1.9569	cytoskeletal part	14	696	cellular component
2.1927802711725235	3.4188	sequence-specific DNA binding	20	579	molecular function
2.1918027877807615	2.0661	metal ion transport	12	569	biological 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.