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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 5007 in total

Class  : biological process

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)
6.564077854156494	transcription from RNA polymerase III promoter	5.5556	1	19
5.84607458114624	beta-tubulin folding	20.0000		5
	tubulin folding	14.2857		8
5.835443019866943	fertilization	5.5556	2	30
	oocyte differentiation	100.0000	1	1
	positive regulation of meiosis	50.0000		2
	regulation of exit from mitosis	10.0000		12
	regulation of meiosis	33.3333		3
	single fertilization	6.2500	2	27
5.326116561889648	cellular respiration	5.2632	1	22
	energy derivation by oxidation of organic compounds	1.4085		82
5.230461120605469	lipid modification	3.3333		35
	lipid phosphorylation	8.3333		14
	phosphoinositide phosphorylation	9.0909		13
	phosphoinositide-mediated signaling	1.7857		76
5.197549819946289	fatty acid oxidation	3.2258		32
	hormone-mediated signaling	11.1111		11
	response to hormone stimulus	1.3158		85
4.7113165855407715	alcohol catabolic process	1.3699		96
	carbohydrate catabolic process	1.0638		121
	cellular carbohydrate catabolic process	1.1236		114
	glucose catabolic process	1.6393		79
	glucose metabolic process	0.9615		130
	glycolysis	1.9608		68
	hexose catabolic process	1.4706		89
	hexose metabolic process	0.6944		174
	monosaccharide catabolic process	1.4493		90
	monosaccharide metabolic process	0.6623		182
4.620415210723877	protein amino acid N-linked glycosylation	2.7027		40
4.601345539093018	reproductive process	1.0811	2	225
4.506189823150635	phagocytosis	5.8824	1	18
4.492823123931885	negative regulation of gene expression, epigenetic	6.6667		20
	regulation of gene expression, epigenetic	2.2222		53
4.407965660095215	neuropeptide signaling pathway	1.3333		100
4.105485280354817	humoral immune response	5.4545	4	80
4.079947471618652	insulin receptor signaling pathway	3.4483	1	32
4.046511650085449	establishment of nucleus localization	25.0000	2	6
	mitotic spindle organization and biogenesis	12.5000	1	9
	nuclear membrane organization and biogenesis	33.3333		3
	nuclear migration	50.0000	2
4.037245273590088	transmembrane receptor protein tyrosine phosphatase signaling pathway	14.2857	1	7
3.9217323064804077	embryonic skeletal morphogenesis	40.0000	2	5
	skeletal morphogenesis	18.1818		13
3.895843982696533	Wnt receptor signaling pathway	1.0309	1	109
3.819567561149597	regulation of cell growth	3.2258	4	133
3.8173599243164062	transcription initiation	1.7857	1	68
	transcription initiation from RNA polymerase II promoter	2.9412		39
3.721451759338379	chromatin remodeling	4.4444	2	53
3.7029240131378174	hemopoietic or lymphoid organ development	1.9608	1	66
	myoblast migration	50.0000		2

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.