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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)
6.564077854156494	5.5556	1	transcription from RNA polymerase III promoter	19
5.84607458114624	20.0000		beta-tubulin folding	5
	14.2857		tubulin folding	8
5.835443019866943	100.0000		oocyte differentiation	1
	50.0000		positive regulation of meiosis	2
	33.3333		regulation of meiosis	3
	10.0000		regulation of exit from mitosis	12
	6.2500	2	single fertilization	27
	5.5556		fertilization	30
5.326116561889648	5.2632	1	cellular respiration	22
	1.4085		energy derivation by oxidation of organic compounds	82
5.230461120605469	9.0909		phosphoinositide phosphorylation	13
	8.3333		lipid phosphorylation	14
	3.3333		lipid modification	35
	1.7857		phosphoinositide-mediated signaling	76
5.197549819946289	11.1111		hormone-mediated signaling	11
	3.2258		fatty acid oxidation	32
	1.3158		response to hormone stimulus	85
4.7113165855407715	1.9608		glycolysis	68
	1.6393		glucose catabolic process	79
	1.4706		hexose catabolic process	89
	1.4493		monosaccharide catabolic process	90
	1.3699		alcohol catabolic process	96
	1.1236		cellular carbohydrate catabolic process	114
	1.0638		carbohydrate catabolic process	121
	0.9615		glucose metabolic process	130
	0.6944		hexose metabolic process	174
	0.6623		monosaccharide metabolic process	182
4.620415210723877	2.7027		protein amino acid N-linked glycosylation	40
4.601345539093018	1.0811	2	reproductive process	225
4.506189823150635	5.8824	1	phagocytosis	18
4.492823123931885	6.6667		negative regulation of gene expression, epigenetic	20
	2.2222		regulation of gene expression, epigenetic	53
4.407965660095215	1.3333		neuropeptide signaling pathway	100
4.105485280354817	5.4545	4	humoral immune response	80
4.079947471618652	3.4483	1	insulin receptor signaling pathway	32
4.046511650085449	50.0000	2	nuclear migration	3
	33.3333	1	nuclear membrane organization and biogenesis
	25.0000	2	establishment of nucleus localization	6
	12.5000	1	mitotic spindle organization and biogenesis	9
4.037245273590088	14.2857		transmembrane receptor protein tyrosine phosphatase signaling pathway	7
3.9217323064804077	40.0000	2	embryonic skeletal morphogenesis	5
	18.1818		skeletal morphogenesis	13
3.895843982696533	1.0309	1	Wnt receptor signaling pathway	109
3.819567561149597	3.2258	4	regulation of cell growth	133
3.8173599243164062	2.9412	1	transcription initiation from RNA polymerase II promoter	39
	1.7857		transcription initiation	68
3.721451759338379	4.4444	2	chromatin remodeling	53
3.7029240131378174	50.0000	1	myoblast migration	2
	11.1111		thymus development	10

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.