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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 125 to 174 of 8866 in total

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