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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 5007 in total

Class  : biological process

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)
3.7029240131378174	striated muscle development	2.7778	1	38
	thymus development	11.1111		10
3.595149040222168	negative regulation of cell growth	7.6923	3	41
	negative regulation of growth	5.8824		57
3.594250440597534	cell migration	0.9259	2	248
3.575074315071106	axonogenesis	4.4444		49
	cell part morphogenesis	3.7736		59
	cell projection morphogenesis
	neurite morphogenesis
3.485576868057251	axon guidance	1.4286	1	80
3.4853661954402924	microtubule cytoskeleton organization and biogenesis	5.2632	5	87
3.400171995162964	cellular structure morphogenesis	1.8987	3	176
3.3986358642578125	second-messenger-mediated signaling	2.4691	5	201
3.398496985435486	spindle organization and biogenesis	10.0000	2	23
3.3942748308181763	glycerophospholipid metabolic process	3.1746		72
	phosphoinositide metabolic process	4.3478		52
	phospholipid metabolic process	1.5038		155
3.367248058319092	interaction with host	5.5556	1	18
	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
3.313642740249634	acylglycerol biosynthetic process	16.6667
	acylglycerol metabolic process	5.0000		28
	glycerol ether biosynthetic process	14.2857		8
	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
	triacylglycerol biosynthetic process	25.0000		4
	triacylglycerol metabolic process	5.8824		23
3.290644884109497	liver development	7.1429		15
3.284923235575358	membrane organization and biogenesis	1.2876	3	252
3.2791879177093506	response to pain	12.5000	1	8
	sensory perception of pain	9.0909		11
3.1892552375793457	fatty acid metabolic process	1.3072	2	172
3.175950493131365	chromosome organization and biogenesis (sensu Eukaryota)	2.0349	10	496

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.