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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 3909 to 3958 of 5007 in total

% Affected Genes  : no value
Average Regulation (ratio)  : no value
Would Be Affected (#genes)  : no value
Class  : biological process

Class Size (#genes)	Class
6	tetrahydrobiopterin biosynthetic process
	tissue morphogenesis
	transcription-coupled nucleotide-excision repair
	tRNA transcription from RNA polymerase III promoter
	tryptophan metabolic process
	tyrosine catabolic process
	V(D)J recombination
	vacuolar transport
	valyl-tRNA aminoacylation
	vascular endothelial growth factor receptor signaling pathway
	viral reproduction
7	acetylcholine receptor signaling, muscarinic pathway
	actin cytoskeleton reorganization
	activation of innate immune response
	amyloid precursor protein catabolic process
	anion homeostasis
	ATP-dependent proteolysis
	B cell receptor signaling pathway
	CD4-positive, alpha beta T cell differentiation
	cellular extravasation
	cellular pH reduction
	cholesterol catabolic process
	chondroitin sulfate biosynthetic process
	chondroitin sulfate metabolic process
	coenzyme A metabolic process
	defense response to Gram-positive bacterium
	deoxyribonucleotide biosynthetic process
	detection of mechanical stimulus
	disaccharide metabolic process
	DNA integration
	dopamine receptor, adenylate cyclase activating pathway
	drug metabolic process
	embryonic placenta development
	endocrine process
	endosome organization and biogenesis
	endothelial cell differentiation
	entry into cell of other organism during symbiotic interaction
	entry into host
	entry into host cell
	entry into other organism during symbiotic interaction
	entry of virus into host cell
	epithelial cell proliferation
	female gonad development
	galactose metabolic process
	glucan catabolic process
	glycine catabolic process
	glycoprotein biosynthetic process
	hemocyte development
	hyperosmotic response
	imprinting

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.