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 [...,...].
Class Size (#genes) Average Regulation (ratio) % Affected Genes Would Be Affected (#genes) Class Class affected Microarray Measured (#genes) Accession
Results: HTML CSV LaTeX Showing element 1 to 50 of 173 in total 
Class	biological process

Class Size (#genes)	Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	
107	2.329086923599243	5.1546	6	embryonic morphogenesis	
117	2.6894871592521667	5.7692	7	muscle development	
142	2.1655175536870956	6.3492	9	protein amino acid dephosphorylation	
142	1.632481078306834	4.7244	7	mitosis	
158	2.1655175536870956	5.7143	9	dephosphorylation	
164	2.267966568470001	3.9735	7	transmembrane receptor protein tyrosine kinase signaling pathway	
170	1.3052469968795777	3.3333	6	regulation of cell differentiation	
192	2.6829177481787547	3.9773	8	regulation of growth	
195	2.9956377029418944	2.9412	6	chromatin modification	
206	2.844642996788025	2.9070	6	nucleocytoplasmic transport	
208	1.8230999537876673	3.7234	8	RNA splicing	
211	2.7829527854919434	2.8249	6	visual perception	
212	2.7829527854919434	2.8090	6	sensory perception of light stimulus	
216	2.4113256633281708	4.7059	10	response to freezing	
217	2.4113256633281708	4.6784	10	homoiothermy	
222	1.3425244291623433	3.0303	7	cell division	
226	2.6329536702897816	5.0000	11	response to cold	
226	2.4113256633281708	4.4444	10	thermoregulation	
229	1.6556044340133667	2.6596	6	anion transport	
229	1.6467143297195435	3.4146	8	cell cycle phase	
230	2.3925783783197403	3.8095	9	enzyme linked receptor protein signaling pathway	
231	3.0316067695617677	2.7174	6	microtubule-based process	
236	1.7727066993713378	2.4510	6	regulation of protein kinase activity	
242	1.7531960964202882	2.3364	6	mRNA processing	
243	1.7727066993713378	2.3810	6	regulation of kinase activity	
247	1.7727066993713378	2.3364	6	regulation of transferase activity	
249	2.6329536702897816	4.4554	11	response to temperature stimulus	
250	1.4007941484451294	2.3585	6	positive regulation of apoptosis	
252	1.4007941484451294	2.3364	6	positive regulation of programmed cell death	
260	1.368695902824402	2.2321	6	chemical homeostasis	
264	2.2164768129587173	3.4335	9	organ morphogenesis	
272	1.9144784212112427	2.0661	6	positive regulation of cell proliferation	
275	1.7971266508102417	2.1368	6	lipid biosynthetic process	
276	1.3052469968795777	2.0492	6	regulation of developmental process	
287	1.8477724552154542	2.1930	6	cell-cell adhesion	
289	1.7531960964202882	1.9841	6	mRNA metabolic process	
292	2.4153901100158692	2.0161	6	potassium ion transport	
314	1.575242853164673	1.8727	6	amino acid metabolic process	
318	2.6086528982434953	2.9289	9	inflammatory response	
321	2.2348088707242693	2.5271	8	nervous system development	
325	2.4346015453338623	1.8051	6	negative regulation of transcription	
335	1.9949067831039429	2.0833	7	protein complex assembly	
337	1.6523104111353557	2.0202	7	response to DNA damage stimulus	
338	2.3975469536251492	2.9801	10	positive regulation of transcription	
347	2.3975469536251492	2.8939	10	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	
358	2.4850547462701797	2.9197	10	response to wounding	
358	2.2540424267450967	1.9608	7	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	
370	2.046714186668396	2.5078	9	cell proliferation	
378	2.3798144817352296	3.2258	12	alcohol metabolic process	
379	2.8815125972032547	2.4922	9	apoptosis	

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/