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 Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 125 to 174 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
3.485576868057251	1.4286	1	80	axon guidance	biological process
3.4853661954402924	5.2632	5	87	microtubule cytoskeleton organization and biogenesis
3.451416552066803	12.5000	2	19	nucleoside transporter activity	molecular function
	8.6957		26	nucleobase, nucleoside, nucleotide and nucleic acid transporter activity
3.4141530990600586	2.3810	1	52	voltage-gated calcium channel activity
3.400171995162964	1.8987	3	176	cellular structure morphogenesis	biological process
3.3986358642578125	2.4691	5	201	second-messenger-mediated signaling
3.398496985435486	10.0000	2	23	spindle organization and biogenesis
3.397643566131592	33.3333	1	3	junctional membrane complex	cellular component
	6.2500		21	sarcoplasmic reticulum
	4.7619			Z disc
	3.0303		37	structural constituent of muscle	molecular function
3.3942748308181763	4.3478	2	52	phosphoinositide metabolic process	biological process
	3.1746		72	glycerophospholipid metabolic process
	1.5038		155	phospholipid metabolic process
3.367248058319092	100.0000	1	1	negative regulation of antiviral response
				negative regulation of antiviral response by host
				positive regulation of viral protein levels in host cell
				regulation of viral protein levels in host cell
	50.0000	2	3	positive regulation of viral genome replication
				regulation of viral transcription
			4	regulation of antiviral response by host
	33.3333		5	positive regulation of viral life cycle
				regulation of antiviral response
	20.0000		10	regulation of viral genome replication
	14.2857	1	7	virus-host interaction
	11.1111	2	15	regulation of viral life cycle
	5.5556	1	18	interaction with host
	3.8462		30	viral reproductive process
	3.0303		36	double-stranded RNA binding	molecular function
	2.1277		56	interspecies interaction between organisms	biological process
				symbiosis, encompassing mutualism through parasitism
	0.9346		131	multi-organism process
3.3235580921173096	4.0000		37	aspartic-type endopeptidase activity	molecular function
3.313642740249634	50.0000	3	5	diacylglycerol O-acyltransferase activity
	33.3333	2	6	2-acylglycerol O-acyltransferase activity
	25.0000	1	4	triacylglycerol biosynthetic process	biological process
	16.6667		7	acylglycerol biosynthetic process
				neutral lipid biosynthetic process
	14.2857		8	glycerol ether biosynthetic process
				glycerolipid biosynthetic process
	10.0000	2	18	acylglycerol O-acyltransferase activity	molecular function
	5.8824	1	23	triacylglycerol metabolic process	biological process
	5.0000		28	acylglycerol metabolic process
				neutral lipid metabolic process
	4.7619		29	glycerolipid metabolic process
	4.5455		30	glycerol ether metabolic process
	4.0000		36	O-acyltransferase activity	molecular function
3.290644884109497	7.1429		15	liver development	biological process
	3.8462		28	RNA polymerase II transcription factor activity, enhancer binding	molecular function

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.