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)	affected	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 101 to 150 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)	Class
3.721451759338379	4.4444	chromatin remodeling	2	53	biological process
3.7029240131378174	50.0000	myoblast migration	1	2
	11.1111	thymus development		10
	2.7778	striated muscle development		38
	1.9608	hemopoietic or lymphoid organ development		66
3.6717275778452554	2.0690	acyltransferase activity	4	180	molecular function
	2.0408	transferase activity, transferring groups other than amino-acyl groups		182
	1.8519	transferase activity, transferring acyl groups		208
3.660576820373535	11.1111	extracellular matrix binding	1	10
		latrotoxin receptor activity
3.595149040222168	7.6923	negative regulation of cell growth	3	41	biological process
	5.8824	negative regulation of growth		57
3.594250440597534	0.9259	cell migration	2	248
3.575074315071106	4.4444	axonogenesis		49
	3.7736	cell part morphogenesis		59
		cell projection morphogenesis
		neurite morphogenesis
3.551537334918976	3.7383	translation regulator activity	5	129	molecular function
3.5441412925720215	100.0000	interleukin-18 receptor complex	1	1	cellular component
	50.0000	interleukin-1 receptor complex	2	3
	33.3333	Toll binding	1		molecular function
3.5221519470214844	0.8130	melanocortin receptor activity	2	196
3.485576868057251	33.3333	axon guidance receptor activity		6
	6.6667	ephrin receptor activity	1	18
	1.4286	axon guidance		80	biological process
3.4853661954402924	5.2632	microtubule cytoskeleton organization and biogenesis	5	87
3.451416552066803	12.5000	nucleoside transporter activity	2	19	molecular function
	8.6957	nucleobase, nucleoside, nucleotide and nucleic acid transporter activity		26
3.4141530990600586	2.3810	voltage-gated calcium channel activity	1	52
3.400171995162964	1.8987	cellular structure morphogenesis	3	176	biological process
3.3986358642578125	2.4691	second-messenger-mediated signaling	5	201
3.398496985435486	10.0000	spindle organization and biogenesis	2	23
3.397643566131592	33.3333	junctional membrane complex	1	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	phosphoinositide metabolic process	2	52	biological process
	3.1746	glycerophospholipid metabolic process		72
	1.5038	phospholipid metabolic process		155
3.367248058319092	100.0000	negative regulation of antiviral response	1	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	positive regulation of viral genome replication	2	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	virus-host interaction	1	7

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.