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	Accession	Microarray Measured (#genes)

Results: HTML CSV LaTeX

Showing element 101 to 150 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
20.0000	2.6936354637145996	1	5	retinoic acid receptor signaling pathway
	2.611353635787964			DNA damage response, detection of DNA damage
	2.0820770263671875		7	hyaluronan metabolic process
	1.765833854675293	2	12	antigen processing and presentation of endogenous peptide antigen
				antigen processing and presentation of endogenous peptide antigen via MHC class I
	1.6198676824569702	1	5	positive regulation of vasoconstriction
				tyrosine phosphorylation of STAT protein
	1.502064824104309		7	sphingoid biosynthetic process
	1.4955823421478271		5	positive regulation of glial cell differentiation
				positive regulation of gliogenesis
	1.4308764934539795		6	carotenoid metabolic process
				tetraterpenoid metabolic process
	1.3020682334899902		5	positive regulation of receptor mediated endocytosis
	1.3014217615127563			positive regulation of protein ubiquitination
	1.2835599184036255		6	cardiac muscle development
	1.20618736743927		5	ATP hydrolysis coupled proton transport
18.1818	3.9217323064804077	2	13	skeletal morphogenesis
	1.2923074960708618		11	regulation of protein modification
16.6667	3.313642740249634	1	7	acylglycerol biosynthetic process
				neutral lipid biosynthetic process
	2.8703815937042236		8	sarcomere organization
	1.9814876317977905		7	isotype switching
				somatic diversification of immunoglobulins during immune response
				somatic recombination of immunoglobulin genes during immune response
	1.765833854675293	2	14	antigen processing and presentation of endogenous antigen
	1.7265567779541016	1	6	ER overload response
	1.6198676824569702			elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)
	1.4992291927337646			platelet-derived growth factor receptor signaling pathway
	1.4955823421478271			positive regulation of osteoblast differentiation
	1.4563519954681396			G2/M transition checkpoint
				G2/M transition DNA damage checkpoint
	1.4221534729003906			monoamine transport
	1.3014217615127563	2	9	negative regulation of epithelial cell proliferation
	1.2165690660476685			vesicle targeting
	1.1086714267730713	1	6	positive regulation of hormone secretion
			7	growth hormone secretion
14.2857	5.84607458114624		8	tubulin folding
	4.037245273590088		7	transmembrane receptor protein tyrosine phosphatase signaling pathway
	3.367248058319092			virus-host interaction
	3.313642740249634		8	glycerol ether biosynthetic process
				glycerolipid biosynthetic process
	2.6936354637145996			neural crest cell development
	1.9667253494262695		7	signal peptide processing
	1.769944667816162		8	myoblast fusion
	1.6198676824569702		7	positive regulation of smooth muscle contraction
	1.6066848039627075		8	regulation of cell volume
	1.3381679058074951	2	11	autophagic vacuole formation
	1.3086906671524048	1	7	mitotic cell cycle
	1.20618736743927			energy coupled proton transport, against electrochemical gradient
	1.192122220993042		10	thyroid hormone 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.