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 [...,...].

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class	affected	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 451 to 500 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
3.8462	2.255178689956665	2	58	negative regulation of protein kinase activity
	1.7265567779541016	1	28	response to reactive oxygen species
	1.4955823421478271		29	odontogenesis (sensu Vertebrata)
	1.4308764934539795		30	sterol biosynthetic process
	1.3825213313102722	2	55	cell cycle checkpoint
	1.3332858085632324	1	31	glycoprotein metabolic process
	1.2411396503448486		32	striated muscle contraction
	1.1949561834335327		31	cofactor catabolic process
	1.1086714267730713		34	peptide transport
3.8095	2.3925783783197403	9	230	enzyme linked receptor protein signaling pathway
3.7736	3.575074315071106	2	59	cell part morphogenesis
				cell projection morphogenesis
				neurite morphogenesis
	3.0427030324935913		64	dicarboxylic acid transport
	2.27594193816185	5	126	biopolymer glycosylation
	2.255178689956665	2	59	negative regulation of transferase activity
	1.4206408858299255	3	69	lipoprotein metabolic process
3.7234	1.8230999537876673	8	208	RNA splicing
3.7037	2.4365404844284058	3	75	biopolymer biosynthetic process
	1.9814876317977905	1	32	heterophilic cell adhesion
	1.9050463438034058	2	59	rRNA processing
	1.6074604988098145	1	33	drug transport
	1.320980151494344	4	95	nucleobase, nucleoside, nucleotide and nucleic acid transport
	1.2733992338180542	1	28	neurotransmitter secretion
	1.2048066854476929		29	menstrual cycle phase
	1.1882063150405884		32	respiratory gaseous exchange
3.6585	1.3772193988164265	3	88	positive regulation of developmental process
3.6364	1.8293300867080688		70	transition metal ion transport
3.5714	2.7880274454752603		95	G-protein signaling, coupled to cyclic nucleotide second messenger
	2.3103933334350586	1	34	maintenance of localization
	2.293897867202759		33	pigmentation
	1.9051852226257324	2	64	G-protein signaling, coupled to cAMP nucleotide second messenger
	1.3014217615127563	1	32	regulation of epithelial cell proliferation
	1.258076786994934		30	adult locomotory behavior
	1.2010211944580078		36	iron ion transport
	1.1949561834335327		31	acetyl-CoA metabolic process
	1.192069411277771		33	RNA export from nucleus
	1.1809606552124023		29	regulation of defense response
				regulation of inflammatory response
	1.1431093215942383		31	regulation of neuron differentiation
3.5604	1.8924930147502734	27	746	cell cycle process
3.4884	1.8127822875976562	4	103	extracellular structure organization and biogenesis
3.4483	4.079947471618652	1	32	insulin receptor signaling pathway
	1.9814876317977905		30	B cell differentiation
	1.9399482011795044		41	induction of apoptosis by extracellular signals
	1.4563519954681396		29	DNA damage checkpoint
	1.1809606552124023		32	developmental growth
	1.1431093215942383			regulation of synaptic plasticity
3.4335	2.2164768129587173	9	264	organ morphogenesis
3.4146	1.6467143297195435	8	229	cell cycle phase

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.