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 125 to 174 of 328 in total 
Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Class	
2.3127479553222656	1.4970	6	behavior	398	biological process	
2.312502180275164	2.3114	96	cell communication	4136	biological process	
2.3059755516052247	2.2085	64	intracellular organelle part	2892	cellular component	
2.3059755516052247	2.2017	64	organelle part	2900	cellular component	
2.3038527108075324	2.4081	66	developmental process	2739	biological process	
2.3028621958649675	2.4798	65	DNA binding	2641	molecular function	
2.299432896077633	1.8561	20	integral to plasma membrane	1060	cellular component	
2.299432896077633	1.8286	20	intrinsic to plasma membrane	1077	cellular component	
2.2985232734680174	2.5907	70	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2698	biological process	
2.28793443441391	2.6247	11	positive regulation of cellular metabolic process	429	biological process	
2.28793443441391	2.4631	11	positive regulation of metabolic process	456	biological process	
2.2792132452352725	2.5000	96	nucleic acid binding	3858	molecular function	
2.2737072706222534	2.2364	17	lipid metabolic process	752	biological process	
2.2681225514251913	2.4354	179	protein binding	7366	molecular function	
2.267966568470001	3.9735	7	transmembrane receptor protein tyrosine kinase signaling pathway	164	biological process	
2.2671763740532787	2.3725	374	cellular_component	15762	cellular component	
2.2670372059712043	2.4610	72	regulation of cellular metabolic process	2913	biological process	
2.2664323395275208	2.4356	452	all	18539	universal	
2.266423319776853	2.9091	28	cell fraction	972	cellular component	
2.2609615601026096	2.4030	18	peptidase activity	734	molecular function	
2.2604436332529243	2.2267	14	response to external stimulus	634	biological process	
2.2601398825645447	1.5228	7	monovalent inorganic cation transport	464	biological process	
2.259431820927244	2.3913	401	molecular_function	16757	molecular function	
2.2576280551010304	2.3831	352	cell part	14761	cellular component	
2.2540424267450967	1.9608	7	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	358	biological process	
2.252760338363143	2.4522	294	cellular process	11986	biological process	
2.248631090488074	2.4047	73	regulation of metabolic process	3018	biological process	
2.246480769722174	2.4413	377	biological_process	15431	biological process	
2.243723976612091	2.0202	15	macromolecule biosynthetic process	762	biological process	
2.241470267334763	2.4400	319	binding	13082	molecular function	
2.2348088707242693	2.5271	8	nervous system development	321	biological process	
2.2326475211552212	1.9608	8	negative regulation of cellular metabolic process	414	biological process	
2.231512101073014	3.0400	22	membrane fraction	739	cellular component	
2.2257004976272583	1.8248	9	olfactory receptor activity	497	molecular function	
2.2204760638150303	1.6923	14	extracellular region part	826	cellular component	
2.220401409599516	2.2099	53	zinc ion binding	2403	molecular function	
2.216642654982189	2.4279	192	intracellular organelle	7902	cellular component	
2.216642654982189	2.4275	192	organelle	7904	cellular component	
2.2164768129587173	3.4335	9	organ morphogenesis	264	biological process	
2.215940025315356	2.4157	170	intracellular membrane-bound organelle	7030	cellular component	
2.215940025315356	2.4157	170	membrane-bound organelle	7030	cellular component	
2.210925724557651	2.3834	239	intracellular part	10046	cellular component	
2.2093183655257618	2.3335	137	catalytic activity	5858	molecular function	
2.2058627247810363	2.0161	23	negative regulation of cellular process	1164	biological process	
2.2058627247810363	1.8957	23	negative regulation of biological process	1238	biological process	
2.201751559972763	1.8244	23	G-protein coupled receptor activity	1284	molecular function	
2.201178240776062	3.3727	24	hydrolase activity, acting on ester bonds	723	molecular function	
2.195966625213623	1.9569	14	cytoskeletal part	696	cellular component	
2.1927802711725235	3.4188	20	sequence-specific DNA binding	579	molecular function	
2.1918027877807615	2.0661	12	metal ion transport	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.
- http://analysis.yellowcouch.org/