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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 5007 in total

Class  : biological process

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

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.