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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class	Would Be Affected (#genes)	Class Size (#genes)
16.6667	1.765833854675293	antigen processing and presentation of endogenous antigen	2	14
	1.7265567779541016	ER overload response	1	6
	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	negative regulation of epithelial cell proliferation	2	9
	1.2165690660476685	vesicle targeting
	1.1086714267730713	growth hormone secretion	1	7
		positive regulation of hormone secretion		6
14.2857	5.84607458114624	tubulin folding		8
	4.037245273590088	transmembrane receptor protein tyrosine phosphatase signaling pathway		7
	3.367248058319092	virus-host interaction
	3.313642740249634	glycerol ether biosynthetic process		8
		glycerolipid biosynthetic process
	2.6936354637145996	neural crest cell development
	1.9667253494262695	signal peptide processing		7
	1.769944667816162	myoblast fusion		8
	1.6198676824569702	positive regulation of smooth muscle contraction		7
	1.6066848039627075	regulation of cell volume		8
	1.3381679058074951	autophagic vacuole formation	2	11
	1.3086906671524048	mitotic cell cycle	1	7
	1.20618736743927	energy coupled proton transport, against electrochemical gradient
	1.192122220993042	thyroid hormone metabolic process		10
	1.1913443803787231	determination of anterior/posterior axis, embryo		9
		embryonic axis specification
	1.1195629835128784	retrograde vesicle-mediated transport, Golgi to ER		10
	1.1086714267730713	regulation of cAMP metabolic process		9
13.3333	3.1701605319976807	nuclear organization and biogenesis	2	17
	1.5622674822807312	fibroblast growth factor receptor signaling pathway		15
12.5000	4.046511650085449	mitotic spindle organization and biogenesis	1	9
	3.2791879177093506	response to pain		8
	2.8703815937042236	response to calcium ion		9
	2.4365404844284058	translational elongation	4	32
	2.104278087615967	negative regulation of amino acid metabolic process	1	8
		negative regulation of protein amino acid phosphorylation
	1.9814876317977905	B cell proliferation
	1.9514372944831848	vitamin A metabolic process	2	16
	1.765833854675293	antigen processing and presentation of peptide antigen via MHC class I	4	31
	1.6198676824569702	positive regulation of muscle contraction	1	9
	1.4955823421478271	regulation of glial cell differentiation		8
		regulation of gliogenesis
		regulation of osteoblast differentiation		9
	1.4221534729003906	neurotransmitter uptake		8
	1.3020682334899902	regulation of receptor mediated endocytosis
	1.3014217615127563	inner ear development
	1.2983962297439575	positive regulation of mitosis	2	15
	1.2746148109436035	thyroid gland development	1	9

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.