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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 173 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)
2.4113256633281708	4.7059	response to freezing	10	216
	4.6784	homoiothermy		217
	4.4444	thermoregulation		226
2.408202938131384	2.6038	biopolymer metabolic process	89	3425
2.403050871690114	3.0060	response to stress	37	1226
2.3975469536251492	2.9801	positive regulation of transcription	10	338
	2.8939	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		347
2.395317418234689	2.2307	cell surface receptor linked signal transduction	46	2077
2.3925783783197403	3.8095	enzyme linked receptor protein signaling pathway	9	230
2.3858967367693675	2.4996	cellular metabolic process	181	7233
2.383645436980508	2.1318	cellular lipid metabolic process	13	619
2.3798144817352296	3.2258	alcohol metabolic process	12	378
2.3753860882350377	2.3133	signal transduction	88	3816
2.374769774137759	2.4068	macromolecule metabolic process	130	5408
2.3732517415826972	2.5375	regulation of transcription, DNA-dependent	62	2448
2.365392540051387	2.5312	cellular protein metabolic process	84	3325
	2.4857	cellular macromolecule metabolic process		3377
2.3636351216514155	2.5270	metabolic process	208	8234
2.3607054107329426	2.6235	protein transport	20	768
	2.4781	establishment of protein localization		810
2.357159194284982	2.4343	primary metabolic process	178	7318
2.329086923599243	5.1546	embryonic morphogenesis	6	107
2.328269682611738	2.5307	protein metabolic process	90	3555
2.319896697998047	2.5057	intracellular protein transport	13	534
2.3178554457061145	2.6245	regulation of transcription	69	2628
2.3127479553222656	1.4970	behavior	6	398
2.312502180275164	2.3114	cell communication	96	4136
2.3038527108075324	2.4081	developmental process	66	2739
2.2985232734680174	2.5907	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	70	2698
2.28793443441391	2.6247	positive regulation of cellular metabolic process	11	429
	2.4631	positive regulation of metabolic process		456
2.2737072706222534	2.2364	lipid metabolic process	17	752
2.267966568470001	3.9735	transmembrane receptor protein tyrosine kinase signaling pathway	7	164
2.2670372059712043	2.4610	regulation of cellular metabolic process	72	2913
2.2604436332529243	2.2267	response to external stimulus	14	634
2.2601398825645447	1.5228	monovalent inorganic cation transport	7	464
2.2540424267450967	1.9608	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		358
2.252760338363143	2.4522	cellular process	294	11986
2.248631090488074	2.4047	regulation of metabolic process	73	3018
2.246480769722174	2.4413	biological_process	377	15431
2.243723976612091	2.0202	macromolecule biosynthetic process	15	762
2.2348088707242693	2.5271	nervous system development	8	321
2.2326475211552212	1.9608	negative regulation of cellular metabolic process		414
2.2164768129587173	3.4335	organ morphogenesis	9	264
2.2058627247810363	2.0161	negative regulation of cellular process	23	1164
	1.8957	negative regulation of biological process		1238
2.1918027877807615	2.0661	metal ion transport	12	569
2.1811264465595115	2.6103	anatomical structure development	33	1273
2.1725611826952766	2.2398	establishment of cellular localization	20	914
2.1655175536870956	6.3492	protein amino acid dephosphorylation	9	142

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.