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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)
3.367248058319092	33.3333	positive regulation of viral life cycle	2	5
		regulation of antiviral response
	20.0000	regulation of viral genome replication		10
	14.2857	virus-host interaction	1	7
	11.1111	regulation of viral life cycle	2	15
	5.5556	interaction with host	1	18
	3.8462	viral reproductive process		30
	2.1277	interspecies interaction between organisms		56
		symbiosis, encompassing mutualism through parasitism
	0.9346	multi-organism process		131
3.313642740249634	25.0000	triacylglycerol biosynthetic process		4
	16.6667	acylglycerol biosynthetic process		7
		neutral lipid biosynthetic process
	14.2857	glycerol ether biosynthetic process		8
		glycerolipid biosynthetic process
	5.8824	triacylglycerol metabolic process		23
	5.0000	acylglycerol metabolic process		28
		neutral lipid metabolic process
	4.7619	glycerolipid metabolic process		29
	4.5455	glycerol ether metabolic process		30
3.290644884109497	7.1429	liver development		15
3.284923235575358	1.2876	membrane organization and biogenesis	3	252
3.2791879177093506	12.5000	response to pain	1	8
	9.0909	sensory perception of pain		11
3.1892552375793457	1.3072	fatty acid metabolic process	2	172
3.175950493131365	2.5000	establishment and/or maintenance of chromatin architecture	10	416
	2.4561	DNA packaging		422
	2.0349	chromosome organization and biogenesis (sensu Eukaryota)		496
3.1701605319976807	13.3333	nuclear organization and biogenesis	2	17
3.1123706102371216	1.6260	response to other organism	3	209
3.0782742261886598	2.2026	defense response	15	680
3.0503673553466797	20.0000	substrate-bound cell migration, cell extension	1	5
	1.8519	cell projection biogenesis		60
	1.1765	cell projection organization and biogenesis		94
	0.9259	cell morphogenesis		120
3.0427030324935913	3.7736	dicarboxylic acid transport	2	64
3.0316067695617677	2.7174	microtubule-based process	6	231
2.9956377029418944	2.9412	chromatin modification		195
2.9439388116200766	1.5385	negative regulation of apoptosis	4	237
	1.5152	negative regulation of programmed cell death		240
2.941256210207939	2.1858	chromosome organization and biogenesis	11	519
2.938953399658203	6.2500	I-kappaB kinase/NF-kappaB cascade	1	20
2.9275668263435364	1.9417	skeletal development	2	119
2.9041290283203125	1.3423	endocytosis		162
	1.2903	membrane invagination		168
2.8815125972032547	2.4922	apoptosis	9	379
	2.4845	programmed cell death		381
2.8703815937042236	16.6667	sarcomere organization	1	8
	12.5000	response to calcium ion		9
2.8696537017822266	3.2258	DNA topological change		33

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.