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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

% Affected Genes	Class	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)
6.3492	protein amino acid dephosphorylation	2.1655175536870956	142	9
5.7692	muscle development	2.6894871592521667	117	7
5.7143	dephosphorylation	2.1655175536870956	158	9
5.1546	embryonic morphogenesis	2.329086923599243	107	6
5.0000	response to cold	2.6329536702897816	226	11
4.7244	mitosis	1.632481078306834	142	7
4.7059	response to freezing	2.4113256633281708	216	10
4.6784	homoiothermy		217
4.4554	response to temperature stimulus	2.6329536702897816	249	11
4.4444	thermoregulation	2.4113256633281708	226	10
4.3573	regulation of progression through cell cycle	1.8484420895576477	535	23
4.3197	regulation of cell cycle		539
3.9773	regulation of growth	2.6829177481787547	192	8
3.9735	transmembrane receptor protein tyrosine kinase signaling pathway	2.267966568470001	164	7
3.8095	enzyme linked receptor protein signaling pathway	2.3925783783197403	230	9
3.7234	RNA splicing	1.8230999537876673	208	8
3.5604	cell cycle process	1.8924930147502734	746	27
3.4335	organ morphogenesis	2.2164768129587173	264	9
3.4146	cell cycle phase	1.6467143297195435	229	8
3.3333	regulation of cell differentiation	1.3052469968795777	170	6
3.2258	alcohol metabolic process	2.3798144817352296	378	12
3.0968	phosphate metabolic process	2.4829982866843543	890	28
	phosphorus metabolic process
3.0405	protein modification process	2.470501118236118	1721	52
3.0303	cell cycle	1.6056334376335144	458	14
	cell division	1.3425244291623433	222	7
3.0060	response to stress	2.403050871690114	1226	37
2.9801	positive regulation of transcription	2.3975469536251492	338	10
2.9680	regulation of transcription from RNA polymerase II promoter	2.46775693159837	499	15
2.9529	post-translational protein modification	2.4479837675352356	1442	43
2.9412	chromatin modification	2.9956377029418944	195	6
2.9393	biopolymer modification	2.470501118236118	1780	52
2.9289	inflammatory response	2.6086528982434953	318	9
2.9197	response to wounding	2.4850547462701797	358	10
2.9070	nucleocytoplasmic transport	2.844642996788025	206	6
2.8939	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2.3975469536251492	347	10
2.8736	response to abiotic stimulus	2.530326783657074	416	12
2.8646	ubiquitin cycle	2.5862315134568648	443	13
2.8333	anatomical structure morphogenesis	2.1418599311043236	686	19
2.8249	visual perception	2.7829527854919434	211	6
2.8090	sensory perception of light stimulus		212
2.7174	microtubule-based process	3.0316067695617677	231
2.6820	intracellular signaling cascade	2.7678764888218472	1217	33
2.6596	anion transport	1.6556044340133667	229	6
2.6362	transcription	2.630213709672292	1588	42
2.6247	positive regulation of cellular metabolic process	2.28793443441391	429	11
2.6245	regulation of transcription	2.3178554457061145	2628	69
2.6235	protein transport	2.3607054107329426	768	20
2.6201	immune response	2.6820639967918396	735	19
2.6103	anatomical structure development	2.1811264465595115	1273	33

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.