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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#genes)	Class	% Affected Genes
6	3.0316067695617677	231	microtubule-based process	2.7174
	2.9956377029418944	195	chromatin modification	2.9412
	2.844642996788025	206	nucleocytoplasmic transport	2.9070
	2.7829527854919434	211	visual perception	2.8249
		212	sensory perception of light stimulus	2.8090
	2.745920252799988	544	carbohydrate metabolic process	1.1390
	2.4346015453338623	325	negative regulation of transcription	1.8051
	2.4153901100158692	292	potassium ion transport	2.0161
	2.329086923599243	107	embryonic morphogenesis	5.1546
	2.3127479553222656	398	behavior	1.4970
	1.9687834978103638	559	cellular catabolic process	1.0870
		704	catabolic process	0.8741
	1.9144784212112427	272	positive regulation of cell proliferation	2.0661
	1.8477724552154542	287	cell-cell adhesion	2.1930
	1.7971266508102417	275	lipid biosynthetic process	2.1368
	1.7727066993713378	236	regulation of protein kinase activity	2.4510
		243	regulation of kinase activity	2.3810
		247	regulation of transferase activity	2.3364
	1.7531960964202882	242	mRNA processing
		289	mRNA metabolic process	1.9841
	1.6556044340133667	229	anion transport	2.6596
	1.575242853164673	314	amino acid metabolic process	1.8727
	1.4007941484451294	250	positive regulation of apoptosis	2.3585
		252	positive regulation of programmed cell death	2.3364
	1.368695902824402	260	chemical homeostasis	2.2321
	1.3052469968795777	170	regulation of cell differentiation	3.3333
		276	regulation of developmental process	2.0492
7	2.6894871592521667	117	muscle development	5.7692
	2.267966568470001	164	transmembrane receptor protein tyrosine kinase signaling pathway	3.9735
	2.2601398825645447	464	monovalent inorganic cation transport	1.5228
	2.2540424267450967	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.9608
	1.9949067831039429	335	protein complex assembly	2.0833
	1.683560033639272	501	regulation of catalytic activity	1.4634
	1.6523104111353557	337	response to DNA damage stimulus	2.0202
	1.632481078306834	142	mitosis	4.7244
	1.5113894144694011	388	amino acid and derivative metabolic process	1.8293
	1.3425244291623433	222	cell division	3.0303
8	2.6829177481787547	192	regulation of growth	3.9773
	2.2348088707242693	321	nervous system development	2.5271
	2.2326475211552212	414	negative regulation of cellular metabolic process	1.9608
	2.158773183822632	428	response to endogenous stimulus	1.8421
	1.8230999537876673	208	RNA splicing	3.7234
	1.6467143297195435	229	cell cycle phase	3.4146
	1.6290612050465174	527	regulation of a molecular function	1.6092
	1.5929162161690849	463	amine metabolic process	1.7949
		484	nitrogen compound metabolic process	1.7157
	1.4910563230514526	514	electron transport	1.5748
9	2.8815125972032547	379	apoptosis	2.4922
		381	programmed cell death	2.4845
	2.6086528982434953	318	inflammatory response	2.9289

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.