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	Class	Average Regulation (ratio)	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	Class	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)
16.6667	growth hormone secretion	1.1086714267730713	1	7
	isotype switching	1.9814876317977905
	monoamine transport	1.4221534729003906		6
	negative regulation of epithelial cell proliferation	1.3014217615127563	2	9
	neutral lipid biosynthetic process	3.313642740249634	1	7
	platelet-derived growth factor receptor signaling pathway	1.4992291927337646		6
	positive regulation of hormone secretion	1.1086714267730713
	positive regulation of osteoblast differentiation	1.4955823421478271
	sarcomere organization	2.8703815937042236		8
	somatic diversification of immunoglobulins during immune response	1.9814876317977905		7
	somatic recombination of immunoglobulin genes during immune response
	vesicle targeting	1.2165690660476685	2	9
14.2857	autophagic vacuole formation	1.3381679058074951		11
	determination of anterior/posterior axis, embryo	1.1913443803787231	1	9
	embryonic axis specification
	energy coupled proton transport, against electrochemical gradient	1.20618736743927		7
	glycerol ether biosynthetic process	3.313642740249634		8
	glycerolipid biosynthetic process
	mitotic cell cycle	1.3086906671524048		7
	myoblast fusion	1.769944667816162		8
	neural crest cell development	2.6936354637145996
	positive regulation of smooth muscle contraction	1.6198676824569702		7
	regulation of cAMP metabolic process	1.1086714267730713		9
	regulation of cell volume	1.6066848039627075		8
	retrograde vesicle-mediated transport, Golgi to ER	1.1195629835128784		10
	signal peptide processing	1.9667253494262695		7
	thyroid hormone metabolic process	1.192122220993042		10
	transmembrane receptor protein tyrosine phosphatase signaling pathway	4.037245273590088		7
	tubulin folding	5.84607458114624		8
	virus-host interaction	3.367248058319092		7
13.3333	fibroblast growth factor receptor signaling pathway	1.5622674822807312	2	15
	nuclear organization and biogenesis	3.1701605319976807		17
12.5000	antigen processing and presentation of peptide antigen via MHC class I	1.765833854675293	4	31
	B cell proliferation	1.9814876317977905	1	8
	embryonic hindlimb morphogenesis	1.258076786994934		9
	inner ear development	1.3014217615127563		8
	mitotic spindle organization and biogenesis	4.046511650085449		9
	negative regulation of amino acid metabolic process	2.104278087615967		8
	negative regulation of protein amino acid phosphorylation
	neurotransmitter uptake	1.4221534729003906
	positive regulation of mitosis	1.2983962297439575	2	15
	positive regulation of muscle contraction	1.6198676824569702	1	9
	regulation of glial cell differentiation	1.4955823421478271		8
	regulation of gliogenesis
	regulation of osteoblast differentiation			9
	regulation of receptor mediated endocytosis	1.3020682334899902		8
	regulation of T-helper cell differentiation	1.2514674663543701
	response to calcium ion	2.8703815937042236		9
	response to pain	3.2791879177093506		8
	thyroid gland development	1.2746148109436035		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.