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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 5007 in total

Class  : biological process

% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Average Regulation (ratio)	Class
16.6667	1	6	1.4221534729003906	monoamine transport
			1.1086714267730713	positive regulation of hormone secretion
		7	3.313642740249634	acylglycerol biosynthetic process
				neutral lipid biosynthetic process
			1.9814876317977905	isotype switching
				somatic diversification of immunoglobulins during immune response
				somatic recombination of immunoglobulin genes during immune response
			1.1086714267730713	growth hormone secretion
		8	2.8703815937042236	sarcomere organization
	2	9	1.3014217615127563	negative regulation of epithelial cell proliferation
			1.2165690660476685	vesicle targeting
		14	1.765833854675293	antigen processing and presentation of endogenous antigen
14.2857	1	7	4.037245273590088	transmembrane receptor protein tyrosine phosphatase signaling pathway
			3.367248058319092	virus-host interaction
			1.9667253494262695	signal peptide processing
			1.6198676824569702	positive regulation of smooth muscle contraction
			1.3086906671524048	mitotic cell cycle
			1.20618736743927	energy coupled proton transport, against electrochemical gradient
		8	5.84607458114624	tubulin folding
			3.313642740249634	glycerol ether biosynthetic process
				glycerolipid biosynthetic process
			2.6936354637145996	neural crest cell development
			1.769944667816162	myoblast fusion
			1.6066848039627075	regulation of cell volume
		9	1.1913443803787231	determination of anterior/posterior axis, embryo
				embryonic axis specification
			1.1086714267730713	regulation of cAMP metabolic process
		10	1.192122220993042	thyroid hormone metabolic process
			1.1195629835128784	retrograde vesicle-mediated transport, Golgi to ER
	2	11	1.3381679058074951	autophagic vacuole formation
13.3333		15	1.5622674822807312	fibroblast growth factor receptor signaling pathway
		17	3.1701605319976807	nuclear organization and biogenesis
12.5000	1	8	3.2791879177093506	response to pain
			2.104278087615967	negative regulation of amino acid metabolic process
				negative regulation of protein amino acid phosphorylation
			1.9814876317977905	B cell proliferation
			1.4955823421478271	regulation of glial cell differentiation
				regulation of gliogenesis
			1.4221534729003906	neurotransmitter uptake
			1.3020682334899902	regulation of receptor mediated endocytosis
			1.3014217615127563	inner ear development
			1.2514674663543701	regulation of T-helper cell differentiation
		9	4.046511650085449	mitotic spindle organization and biogenesis
			2.8703815937042236	response to calcium ion
			1.6198676824569702	positive regulation of muscle contraction
			1.4955823421478271	regulation of osteoblast differentiation
			1.2746148109436035	thyroid gland development
			1.258076786994934	embryonic hindlimb morphogenesis
	2	15	1.2983962297439575	positive regulation of mitosis
		16	1.9514372944831848	vitamin A metabolic process

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.