Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 51 to 100 of 328 in total 
Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Class	
2.523834652370877	2.8754	10	identical protein binding	363	molecular function	
2.5149934005737307	2.3063	34	intracellular non-membrane-bound organelle	1485	cellular component	
2.5149934005737307	2.3063	34	non-membrane-bound organelle	1485	cellular component	
2.506679137547811	3.0928	10	transcriptional activator activity	331	molecular function	
2.506638288497925	3.0928	7	microtubule	238	cellular component	
2.5005394551489086	1.8711	21	cellular developmental process	1118	biological process	
2.4995227009058	2.3460	9	magnesium ion binding	380	molecular function	
2.4881605356931686	2.5078	9	cation channel activity	370	molecular function	
2.4850547462701797	2.9197	10	response to wounding	358	biological process	
2.4829982866843543	3.0968	28	phosphate metabolic process	890	biological process	
2.4829982866843543	3.0968	28	phosphorus metabolic process	890	biological process	
2.470501118236118	3.0405	52	protein modification process	1721	biological process	
2.470501118236118	2.9393	52	biopolymer modification	1780	biological process	
2.46775693159837	2.9680	15	regulation of transcription from RNA polymerase II promoter	499	biological process	
2.455523896217346	4.7619	13	GTPase activity	270	molecular function	
2.453812837600708	1.9231	11	translation	552	biological process	
2.4517960273302517	2.2569	15	protein kinase activity	672	molecular function	
2.4479837675352356	2.9529	43	post-translational protein modification	1442	biological process	
2.4382004340489707	2.2514	16	sensory perception	732	biological process	
2.4382004340489707	2.2181	16	neurological process	741	biological process	
2.4346015453338623	1.8051	6	negative regulation of transcription	325	biological process	
2.4306948675828823	2.1879	67	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	3075	biological process	
2.43051519464044	2.0821	42	cellular component organization and biogenesis	2008	biological process	
2.4235891212116587	2.3061	13	protein serine/threonine kinase activity	544	molecular function	
2.420156256183163	2.5757	121	nucleus	4692	cellular component	
2.416864479581515	2.3483	34	G-protein coupled receptor protein signaling pathway	1453	biological process	
2.4153901100158692	2.0161	6	potassium ion transport	292	biological process	
2.4113256633281708	4.7059	10	ice binding	216	molecular function	
2.4113256633281708	4.7059	10	response to freezing	216	biological process	
2.4113256633281708	4.7059	10	water binding	216	molecular function	
2.4113256633281708	4.6784	10	homoiothermy	217	biological process	
2.4113256633281708	4.4444	10	thermoregulation	226	biological process	
2.410263843006558	2.0443	47	protein complex	2308	cellular component	
2.4100664528933438	2.2358	13	protein-tyrosine kinase activity	565	molecular function	
2.408202938131384	2.6038	89	biopolymer metabolic process	3425	biological process	
2.403050871690114	3.0060	37	response to stress	1226	biological process	
2.4005173126856487	2.0492	20	oxidoreductase activity	955	molecular function	
2.3990859508514406	2.2422	6	soluble fraction	256	cellular component	
2.3975469536251492	2.9801	10	positive regulation of transcription	338	biological process	
2.3975469536251492	2.8939	10	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	347	biological process	
2.3974582254886627	3.4272	36	transcription factor activity	1038	molecular function	
2.395317418234689	2.2307	46	cell surface receptor linked signal transduction	2077	biological process	
2.3925783783197403	3.8095	9	enzyme linked receptor protein signaling pathway	230	biological process	
2.3858967367693675	2.4996	181	cellular metabolic process	7233	biological process	
2.383645436980508	2.1318	13	cellular lipid metabolic process	619	biological process	
2.3829759624269276	2.1687	11	ion channel activity	494	molecular function	
2.3829759624269276	2.0882	11	alpha-type channel activity	511	molecular function	
2.3829759624269276	2.0362	11	channel or pore class transporter activity	526	molecular function	
2.3798144817352296	3.2258	12	alcohol metabolic process	378	biological process	
2.3753860882350377	2.3133	88	signal transduction	3816	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.
- http://analysis.yellowcouch.org/