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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Class Size (#genes)	% Affected Genes	Class	Average Regulation (ratio)
6	107	5.1546	embryonic morphogenesis	2.329086923599243
	170	3.3333	regulation of cell differentiation	1.3052469968795777
	195	2.9412	chromatin modification	2.9956377029418944
	206	2.9070	nucleocytoplasmic transport	2.844642996788025
	211	2.8249	visual perception	2.7829527854919434
	212	2.8090	sensory perception of light stimulus
	229	2.6596	anion transport	1.6556044340133667
	231	2.7174	microtubule-based process	3.0316067695617677
	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
	250	2.3585	positive regulation of apoptosis	1.4007941484451294
	252	2.3364	positive regulation of programmed cell death
	260	2.2321	chemical homeostasis	1.368695902824402
	272	2.0661	positive regulation of cell proliferation	1.9144784212112427
	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
	325	1.8051	negative regulation of transcription	2.4346015453338623
	398	1.4970	behavior	2.3127479553222656
	544	1.1390	carbohydrate metabolic process	2.745920252799988
	559	1.0870	cellular catabolic process	1.9687834978103638
	704	0.8741	catabolic process
7	117	5.7692	muscle development	2.6894871592521667
	142	4.7244	mitosis	1.632481078306834
	164	3.9735	transmembrane receptor protein tyrosine kinase signaling pathway	2.267966568470001
	222	3.0303	cell division	1.3425244291623433
	335	2.0833	protein complex assembly	1.9949067831039429
	337	2.0202	response to DNA damage stimulus	1.6523104111353557
	358	1.9608	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2.2540424267450967
	388	1.8293	amino acid and derivative metabolic process	1.5113894144694011
	464	1.5228	monovalent inorganic cation transport	2.2601398825645447
	501	1.4634	regulation of catalytic activity	1.683560033639272
8	192	3.9773	regulation of growth	2.6829177481787547
	208	3.7234	RNA splicing	1.8230999537876673
	229	3.4146	cell cycle phase	1.6467143297195435
	321	2.5271	nervous system development	2.2348088707242693
	414	1.9608	negative regulation of cellular metabolic process	2.2326475211552212
	428	1.8421	response to endogenous stimulus	2.158773183822632
	463	1.7949	amine metabolic process	1.5929162161690849
	484	1.7157	nitrogen compound metabolic process
	514	1.5748	electron transport	1.4910563230514526
	527	1.6092	regulation of a molecular function	1.6290612050465174
9	142	6.3492	protein amino acid dephosphorylation	2.1655175536870956
	158	5.7143	dephosphorylation
	230	3.8095	enzyme linked receptor protein signaling pathway	2.3925783783197403

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.