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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

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