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

Results: HTML CSV LaTeX

Showing element 625 to 674 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Would Be Affected (#genes)	Class
1.4450746377309163	2.8302	121	3	calcium ion homeostasis
	2.1429	167	4	di-, tri-valent inorganic cation homeostasis
	2.0408	175		metal ion homeostasis
1.439520239830017	1.6129	242		sexual reproduction
	1.6043	243		reproduction
1.4335074424743652	100.0000	1	1	vacuolar protein catabolic process
1.4308764934539795	25.0000	5		carotenoid biosynthetic process
				terpenoid biosynthetic process
				tetraterpenoid biosynthetic process
	20.0000	6		carotenoid metabolic process
				tetraterpenoid metabolic process
	11.1111	15	2	isoprenoid biosynthetic process
	7.6923		1	terpenoid metabolic process
	5.5556	25		isoprenoid metabolic process
	5.2632	22		cholesterol biosynthetic process
	3.8462	30		sterol biosynthetic process
	2.9412	38		pigment biosynthetic process
	2.6316	42		pigment metabolic process
	1.3514	91		steroid biosynthetic process
1.4288471937179565	1.2500	209	3	regulation of hydrolase activity
1.4221534729003906	100.0000	1	1	serotonin transport
	16.6667	6		monoamine transport
	12.5000	8		neurotransmitter uptake
1.4218664169311523	1.9231	190	4	inorganic anion transport
1.4206408858299255	5.2632	39	2	protein amino acid lipidation
	5.1282	40		lipoprotein biosynthetic process
	3.7736	69	3	lipoprotein metabolic process
1.4074867963790894	1.4493	95	1	phosphate transport
1.4038362503051758	2.6549	129	3	hemostasis
	2.1898	154		regulation of body fluids
1.4007941484451294	2.3585	250	6	positive regulation of apoptosis
	2.3364	252		positive regulation of programmed cell death
1.3985020518302917	5.1282	43	2	cell growth
1.39005708694458	66.6667	3		neural nucleus development
1.3853528201580048	2.5478	186	5	cation homeostasis
	2.4096	196		cell ion homeostasis
	2.1390	221		ion homeostasis
	1.5625	304		cell homeostasis
1.3825213313102722	11.1111	19	2	mitotic checkpoint
	3.8462	55		cell cycle checkpoint
1.3795016606648762	8.1081	48	4	positive regulation of transport
	2.6316	136		regulation of transport
1.3786529898643494	7.1429	32	2	blood vessel development
	6.6667	34		vasculature development
1.377636730670929	1.8519	123		blood coagulation
				coagulation
1.3772193988164265	5.2632	59	3	positive regulation of cell differentiation
	3.6585	88		positive regulation of developmental process
1.3756878972053528	1.5094	308	5	regulation of protein metabolic process
1.371099054813385	1.3333	184	2	cellular protein catabolic process

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.