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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 8866 in total

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
3.485576868057251	ephrin receptor activity	6.6667	1	18	molecular function
3.4853661954402924	microtubule cytoskeleton organization and biogenesis	5.2632	5	87	biological process
3.451416552066803	nucleobase, nucleoside, nucleotide and nucleic acid transporter activity	8.6957	2	26	molecular function
	nucleoside transporter activity	12.5000		19
3.4141530990600586	voltage-gated calcium channel activity	2.3810	1	52
3.400171995162964	cellular structure morphogenesis	1.8987	3	176	biological process
3.3986358642578125	second-messenger-mediated signaling	2.4691	5	201
3.398496985435486	spindle organization and biogenesis	10.0000	2	23
3.397643566131592	junctional membrane complex	33.3333	1	3	cellular component
	sarcoplasmic reticulum	6.2500		21
	structural constituent of muscle	3.0303		37	molecular function
	Z disc	4.7619		21	cellular component
3.3942748308181763	glycerophospholipid metabolic process	3.1746	2	72	biological process
	phosphoinositide metabolic process	4.3478		52
	phospholipid metabolic process	1.5038		155
3.367248058319092	double-stranded RNA binding	3.0303	1	36	molecular function
	interaction with host	5.5556		18	biological process
	interspecies interaction between organisms	2.1277		56
	multi-organism process	0.9346		131
	negative regulation of antiviral response	100.0000		1
	negative regulation of antiviral response by host
	positive regulation of viral genome replication	50.0000	2	3
	positive regulation of viral life cycle	33.3333		5
	positive regulation of viral protein levels in host cell	100.0000	1	1
	regulation of antiviral response	33.3333	2	5
	regulation of antiviral response by host	50.0000		4
	regulation of viral genome replication	20.0000		10
	regulation of viral life cycle	11.1111		15
	regulation of viral protein levels in host cell	100.0000	1	1
	regulation of viral transcription	50.0000	2	3
	symbiosis, encompassing mutualism through parasitism	2.1277	1	56
	viral reproductive process	3.8462		30
	virus-host interaction	14.2857		7
3.3235580921173096	aspartic-type endopeptidase activity	4.0000		37	molecular function
3.313642740249634	2-acylglycerol O-acyltransferase activity	33.3333	2	6
	acylglycerol biosynthetic process	16.6667	1	7	biological process
	acylglycerol metabolic process	5.0000		28
	acylglycerol O-acyltransferase activity	10.0000	2	18	molecular function
	diacylglycerol O-acyltransferase activity	50.0000	3	5
	glycerol ether biosynthetic process	14.2857	1	8	biological process
	glycerol ether metabolic process	4.5455		30
	glycerolipid biosynthetic process	14.2857		8
	glycerolipid metabolic process	4.7619		29
	neutral lipid biosynthetic process	16.6667		7
	neutral lipid metabolic process	5.0000		28
	O-acyltransferase activity	4.0000		36	molecular function
	triacylglycerol biosynthetic process	25.0000		4	biological process
	triacylglycerol metabolic process	5.8824		23
3.290644884109497	liver development	7.1429		15
	RNA polymerase II transcription factor activity, enhancer binding	3.8462		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.