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

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.