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