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 75 to 124 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Class	Would Be Affected (#genes)	Class Size (#genes)	Class
4.046511650085449	33.3333	nuclear membrane organization and biogenesis	1	3	biological process
	25.0000	establishment of nucleus localization	2	6
	12.5000	mitotic spindle organization and biogenesis	1	9
	7.6923	condensed nuclear chromosome		16	cellular component
	5.0000	chromosome, telomeric region		23
	2.3256	nuclear envelope		56
4.037245273590088	14.2857	transmembrane receptor protein tyrosine phosphatase signaling pathway		7	biological process
	5.5556	transmembrane receptor protein phosphatase activity		18	molecular function
		transmembrane receptor protein tyrosine phosphatase activity
3.9968204498291016	1.7857	vascular endothelial growth factor receptor activity		72
	1.0309	GPI anchor binding		119
3.9418493509292603	1.5385	cysteine-type peptidase activity	3	172
3.9217323064804077	40.0000	embryonic skeletal morphogenesis	2	5	biological process
	18.1818	skeletal morphogenesis		13
3.895843982696533	1.0309	Wnt receptor signaling pathway	1	109
3.8507699966430664	100.0000	arylamine N-acetyltransferase activity	2	2	molecular function
	4.5455	N-acetyltransferase activity		52
	4.0000	N-acyltransferase activity		61
	3.7736	acetyltransferase activity		63
3.8397669792175293	5.0000	nuclear matrix	1	21	cellular component
3.819567561149597	3.2258	regulation of cell growth	4	133	biological process
3.8173599243164062	2.9412	transcription initiation from RNA polymerase II promoter	1	39
	1.7857	transcription initiation		68
3.789476911226908	4.4118	structural constituent of cell wall	4	80	molecular function
3.749711751937866	12.5000	glutathione peroxidase activity	1	10
	5.2632	selenium binding	2	31
3.721451759338379	4.4444	chromatin remodeling		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

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.