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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 8866 in total

% Affected Genes	Class	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
100.0000	arylamine N-acetyltransferase activity	3.8507699966430664	2	2	molecular function
	beta-mannosidase activity	1.3332858085632324	1	1
	caudate nucleus development	1.5708750486373901			biological process
	CD40 receptor binding	1.9814876317977905			molecular function
	cyclooxygenase pathway	1.1809606552124023			biological process
	cysteine desulfurase activity	1.1953918933868408			molecular function
	cytoplasmic chromatin	5.835443019866943			cellular component
	dolichyl-phosphate beta-glucosyltransferase activity	1.5431665182113647			molecular function
	GDP-dissociation stimulator activity	1.682999849319458
	granulocyte macrophage colony-stimulating factor receptor complex	1.1882063150405884			cellular component
	growth hormone-releasing hormone receptor binding	1.1086714267730713			molecular function
	interleukin-18 receptor complex	3.5441412925720215			cellular component
	isopentenyl-diphosphate delta-isomerase activity	1.4308764934539795	2	2	molecular function
	leading edge cell differentiation	2.104278087615967	1	1	biological process
	muscle cell fate determination	1.2835599184036255
	N-terminal arginine aminopeptidase activity	1.765833854675293			molecular function
	N-terminal basic amino acid aminopeptidase activity
	N-terminal lysine aminopeptidase activity
	negative regulation of antiviral response	3.367248058319092			biological process
	negative regulation of antiviral response by host
	nose development	1.258076786994934
	nucleus accumbens development	1.20923912525177
	oocyte differentiation	5.835443019866943
	optic cup morphogenesis involved in camera-type eye development	1.20923912525177
	osmosensory signaling pathway	1.6066848039627075
	pericardium development	1.3346540927886963
	positive regulation of astrocyte differentiation	1.4955823421478271
	positive regulation of cyclin-dependent protein kinase activity	1.2769564390182495
	positive regulation of lymphotoxin A biosynthetic process	1.2514674663543701
	positive regulation of viral protein levels in host cell	3.367248058319092
	putamen development	1.5708750486373901
	regulation of lymphotoxin A biosynthetic process	1.2514674663543701
	regulation of viral protein levels in host cell	3.367248058319092
	retinoic acid 4-hydroxylase activity	2.6936354637145996			molecular function
	RNA lariat debranching enzyme activity	1.3741127252578735
	serotonin transport	1.4221534729003906			biological process
	serotonin transporter activity				molecular function
	serotonin:sodium symporter activity
	spindle assembly	2.7504823207855225	2	2	biological process
	synaptic vesicle targeting	1.2165690660476685	1	1
	transport accessory protein activity	1.3020682334899902			molecular function
	vacuolar protein catabolic process	1.4335074424743652			biological process
66.6667	neural nucleus development	1.39005708694458	2	3
50.0000	aldehyde dehydrogenase [NAD(P)+] activity	2.8086023926734924	3	6	molecular function
	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	3.2158093452453613	1	2
	ATP-dependent polynucleotide kinase activity
	cytokinesis after mitosis	1.2983962297439575	3	5	biological process
	deoxyribonuclease II activity	1.1954466104507446	1	2	molecular function
	diacylglycerol O-acyltransferase activity	3.313642740249634	3	5
	endodeoxyribonuclease activity, producing 3'-phosphomonoesters	1.1954466104507446	1	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.