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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Class	Average Regulation (ratio)	% Affected Genes	Class Size (#genes)
6	amino acid metabolic process	1.575242853164673	1.8727	314
	anion transport	1.6556044340133667	2.6596	229
	behavior	2.3127479553222656	1.4970	398
	carbohydrate metabolic process	2.745920252799988	1.1390	544
	catabolic process	1.9687834978103638	0.8741	704
	cell-cell adhesion	1.8477724552154542	2.1930	287
	cellular catabolic process	1.9687834978103638	1.0870	559
	chemical homeostasis	1.368695902824402	2.2321	260
	chromatin modification	2.9956377029418944	2.9412	195
	embryonic morphogenesis	2.329086923599243	5.1546	107
	lipid biosynthetic process	1.7971266508102417	2.1368	275
	microtubule-based process	3.0316067695617677	2.7174	231
	mRNA metabolic process	1.7531960964202882	1.9841	289
	mRNA processing		2.3364	242
	negative regulation of transcription	2.4346015453338623	1.8051	325
	nucleocytoplasmic transport	2.844642996788025	2.9070	206
	positive regulation of apoptosis	1.4007941484451294	2.3585	250
	positive regulation of cell proliferation	1.9144784212112427	2.0661	272
	positive regulation of programmed cell death	1.4007941484451294	2.3364	252
	potassium ion transport	2.4153901100158692	2.0161	292
	regulation of cell differentiation	1.3052469968795777	3.3333	170
	regulation of developmental process		2.0492	276
	regulation of kinase activity	1.7727066993713378	2.3810	243
	regulation of protein kinase activity		2.4510	236
	regulation of transferase activity		2.3364	247
	sensory perception of light stimulus	2.7829527854919434	2.8090	212
	visual perception		2.8249	211
7	amino acid and derivative metabolic process	1.5113894144694011	1.8293	388
	cell division	1.3425244291623433	3.0303	222
	mitosis	1.632481078306834	4.7244	142
	monovalent inorganic cation transport	2.2601398825645447	1.5228	464
	muscle development	2.6894871592521667	5.7692	117
	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	2.2540424267450967	1.9608	358
	protein complex assembly	1.9949067831039429	2.0833	335
	regulation of catalytic activity	1.683560033639272	1.4634	501
	response to DNA damage stimulus	1.6523104111353557	2.0202	337
	transmembrane receptor protein tyrosine kinase signaling pathway	2.267966568470001	3.9735	164
8	amine metabolic process	1.5929162161690849	1.7949	463
	cell cycle phase	1.6467143297195435	3.4146	229
	electron transport	1.4910563230514526	1.5748	514
	negative regulation of cellular metabolic process	2.2326475211552212	1.9608	414
	nervous system development	2.2348088707242693	2.5271	321
	nitrogen compound metabolic process	1.5929162161690849	1.7157	484
	regulation of a molecular function	1.6290612050465174	1.6092	527
	regulation of growth	2.6829177481787547	3.9773	192
	response to endogenous stimulus	2.158773183822632	1.8421	428
	RNA splicing	1.8230999537876673	3.7234	208
9	apoptosis	2.8815125972032547	2.4922	379
	carboxylic acid metabolic process	1.9312101155519485	1.6327	570
	cell motility	2.1474349200725555	2.1390	432

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.