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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)
2.8630340496699014	3.3708	embryonic development	3	98
2.8629825115203857	1.2987	brain development	1	91
2.844642996788025	2.9070	nucleocytoplasmic transport	6	206
2.8162122435039945	2.4658	cell death	11	430
		death
2.812885562578837	1.4706	protein folding	4	266
2.8056000471115112	2.3669	positive regulation of transcription from RNA polymerase II promoter		186
	1.6260	positive regulation of transcription, DNA-dependent		276
2.7880274454752603	3.5714	G-protein signaling, coupled to cyclic nucleotide second messenger	3	95
	3.3333	cyclic-nucleotide-mediated signaling		101
2.7829527854919434	2.8249	visual perception	6	211
	2.8090	sensory perception of light stimulus		212
2.775389830271403	1.4151	sensory perception of smell	5	344
	1.3158	sensory perception of chemical stimulus		378
2.7678764888218472	2.6820	intracellular signaling cascade	33	1217
2.7504823207855225	100.0000	spindle assembly	2	2
	20.0000	centrosome duplication	1	5
	6.2500	centrosome organization and biogenesis		17
		microtubule organizing center organization and biogenesis
2.7469783226648965	10.7143	glycerol metabolic process	4	35
	10.3448	polyol metabolic process		37
2.745920252799988	1.1390	carbohydrate metabolic process	6	544
2.736812561750412	2.8777	negative regulation of transcription from RNA polymerase II promoter	5	165
	1.9900	negative regulation of transcription, DNA-dependent		238
2.7119380235671997	1.8182	cytoskeleton organization and biogenesis	10	531
2.7088398138682046	1.9481	protein-DNA complex assembly	5	265
2.7016990184783936	5.0000	G-protein signaling, adenylate cyclase inhibiting pathway	1	21
2.6960288683573403	2.4064	small GTPase mediated signal transduction	11	442
2.6936354637145996	20.0000	retinoic acid receptor signaling pathway	1	5
	14.2857	neural crest cell development		8
	1.8519	intracellular receptor-mediated signaling pathway		59
	1.5385	anterior/posterior pattern formation		71
	0.9434	regionalization		115
2.6894871592521667	5.7692	muscle development	7	117
2.6829177481787547	3.9773	regulation of growth	8	192
2.6820639967918396	2.6201	immune response	19	735
2.6724539399147034	11.7647	establishment of organelle localization	2	21
2.6627832651138306	0.9709	cellular carbohydrate metabolic process	4	365
2.6506848335266113	3.8462	activation of plasma proteins during acute inflammatory response	2	41
		complement activation
	1.8182	activation of immune response	1	72
	1.4493	positive regulation of immune response		89
	1.4286	positive regulation of immune system process		90
	1.2195	regulation of immune response		103
	1.1905	regulation of immune system process		105
2.6504326661427817	1.6760	response to biotic stimulus	5	296
2.644248050451279	2.1413	organelle organization and biogenesis	26	1204
2.6417386531829834	2.5890	phosphorylation	18	711
2.639615813891093	2.6087	heart development	3	126
2.6354507505893707	2.0101	transcription, DNA-dependent	5	225

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.