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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

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