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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

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