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