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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 173 in total

Class  : biological process

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)
2.4113256633281708	homoiothermy	4.6784	10	217
	response to freezing	4.7059		216
	thermoregulation	4.4444		226
2.408202938131384	biopolymer metabolic process	2.6038	89	3425
2.403050871690114	response to stress	3.0060	37	1226
2.3975469536251492	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2.8939	10	347
	positive regulation of transcription	2.9801		338
2.395317418234689	cell surface receptor linked signal transduction	2.2307	46	2077
2.3925783783197403	enzyme linked receptor protein signaling pathway	3.8095	9	230
2.3858967367693675	cellular metabolic process	2.4996	181	7233
2.383645436980508	cellular lipid metabolic process	2.1318	13	619
2.3798144817352296	alcohol metabolic process	3.2258	12	378
2.3753860882350377	signal transduction	2.3133	88	3816
2.374769774137759	macromolecule metabolic process	2.4068	130	5408
2.3732517415826972	regulation of transcription, DNA-dependent	2.5375	62	2448
2.365392540051387	cellular macromolecule metabolic process	2.4857	84	3377
	cellular protein metabolic process	2.5312		3325
2.3636351216514155	metabolic process	2.5270	208	8234
2.3607054107329426	establishment of protein localization	2.4781	20	810
	protein transport	2.6235		768
2.357159194284982	primary metabolic process	2.4343	178	7318
2.329086923599243	embryonic morphogenesis	5.1546	6	107
2.328269682611738	protein metabolic process	2.5307	90	3555
2.319896697998047	intracellular protein transport	2.5057	13	534
2.3178554457061145	regulation of transcription	2.6245	69	2628
2.3127479553222656	behavior	1.4970	6	398
2.312502180275164	cell communication	2.3114	96	4136
2.3038527108075324	developmental process	2.4081	66	2739
2.2985232734680174	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2.5907	70	2698
2.28793443441391	positive regulation of cellular metabolic process	2.6247	11	429
	positive regulation of metabolic process	2.4631		456
2.2737072706222534	lipid metabolic process	2.2364	17	752
2.267966568470001	transmembrane receptor protein tyrosine kinase signaling pathway	3.9735	7	164
2.2670372059712043	regulation of cellular metabolic process	2.4610	72	2913
2.2604436332529243	response to external stimulus	2.2267	14	634
2.2601398825645447	monovalent inorganic cation transport	1.5228	7	464
2.2540424267450967	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.9608		358
2.252760338363143	cellular process	2.4522	294	11986
2.248631090488074	regulation of metabolic process	2.4047	73	3018
2.246480769722174	biological_process	2.4413	377	15431
2.243723976612091	macromolecule biosynthetic process	2.0202	15	762
2.2348088707242693	nervous system development	2.5271	8	321
2.2326475211552212	negative regulation of cellular metabolic process	1.9608		414
2.2164768129587173	organ morphogenesis	3.4335	9	264
2.2058627247810363	negative regulation of biological process	1.8957	23	1238
	negative regulation of cellular process	2.0161		1164
2.1918027877807615	metal ion transport	2.0661	12	569
2.1811264465595115	anatomical structure development	2.6103	33	1273
2.1725611826952766	establishment of cellular localization	2.2398	20	914
2.1655175536870956	dephosphorylation	5.7143	9	158

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.