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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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

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.