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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 8866 in total

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

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.