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	Would Be Affected (#genes)	Class	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	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
4.046511650085449	33.3333	1	nuclear membrane organization and biogenesis	3	biological process
	25.0000	2	establishment of nucleus localization	6
	12.5000	1	mitotic spindle organization and biogenesis	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	3	cysteine-type peptidase activity	172
3.9217323064804077	40.0000	2	embryonic skeletal morphogenesis	5	biological process
	18.1818		skeletal morphogenesis	13
3.895843982696533	1.0309	1	Wnt receptor signaling pathway	109
3.8507699966430664	100.0000	2	arylamine N-acetyltransferase activity	2	molecular function
	4.5455		N-acetyltransferase activity	52
	4.0000		N-acyltransferase activity	61
	3.7736		acetyltransferase activity	63
3.8397669792175293	5.0000	1	nuclear matrix	21	cellular component
3.819567561149597	3.2258	4	regulation of cell growth	133	biological process
3.8173599243164062	2.9412	1	transcription initiation from RNA polymerase II promoter	39
	1.7857		transcription initiation	68
3.789476911226908	4.4118	4	structural constituent of cell wall	80	molecular function
3.749711751937866	12.5000	1	glutathione peroxidase activity	10
	5.2632	2	selenium binding	31
3.721451759338379	4.4444		chromatin remodeling	53	biological process
3.7029240131378174	50.0000	1	myoblast migration	2
	11.1111		thymus development	10
	2.7778		striated muscle development	38
	1.9608		hemopoietic or lymphoid organ development	66
3.6717275778452554	2.0690	4	acyltransferase activity	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	1	extracellular matrix binding	10
			latrotoxin receptor activity
3.595149040222168	7.6923	3	negative regulation of cell growth	41	biological process
	5.8824		negative regulation of growth	57
3.594250440597534	0.9259	2	cell migration	248
3.575074315071106	4.4444		axonogenesis	49
	3.7736		cell part morphogenesis	59
			cell projection morphogenesis
			neurite morphogenesis
3.551537334918976	3.7383	5	translation regulator activity	129	molecular function
3.5441412925720215	100.0000	1	interleukin-18 receptor complex	1	cellular component
	50.0000	2	interleukin-1 receptor complex	3
	33.3333	1	Toll binding		molecular function
3.5221519470214844	0.8130	2	melanocortin receptor activity	196
3.485576868057251	33.3333		axon guidance receptor activity	6
	6.6667	1	ephrin receptor activity	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.