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)	affected	Class	Class Size (#genes)	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 401 to 450 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)
1.9346576482057571	1.6701	11	generation of precursor metabolites and energy	629
1.9312101155519485	1.6327	9	carboxylic acid metabolic process	570
	1.6227		organic acid metabolic process	573
1.9293138980865479	2.3256	2	central nervous system development	94
1.9220449527104695	3.0303	4	positive regulation of multicellular organismal process	120
1.9144784212112427	2.0661	6	positive regulation of cell proliferation	272
1.9092395901679993	10.5263	2	synaptogenesis	23
1.9051852226257324	3.5714		G-protein signaling, coupled to cAMP nucleotide second messenger	64
	3.3333		cAMP-mediated signaling	68
1.9050463438034058	3.7037		rRNA processing	59
	3.3898		rRNA metabolic process	65
1.9009546041488647	3.2967	3	response to drug	99
1.8924930147502734	3.5604	27	cell cycle process	746
1.8912208477656047	1.6043	3	synaptic transmission	212
1.8862953583399455	2.0408		protein kinase cascade	169
1.8484420895576477	4.3573	23	regulation of progression through cell cycle	535
	4.3197		regulation of cell cycle	539
1.8477724552154542	2.1930	6	cell-cell adhesion	287
1.8458595871925354	2.6490	5	di-, tri-valent inorganic cation transport	181
1.8413102626800537	2.2670	10	RNA processing	448
1.8383450422968184	2.1407	17	biological adhesion	806
			cell adhesion
1.8379053473472595	2.8169	7	chromatin assembly or disassembly	256
1.8293300867080688	3.6364	3	transition metal ion transport	70
1.823113203048706	7.6923	1	glial cell differentiation	15
1.8230999537876673	3.7234	8	RNA splicing	208
1.8127822875976562	7.3171	4	synapse organization and biogenesis	48
	3.4884		extracellular structure organization and biogenesis	103
1.7971266508102417	2.1368	6	lipid biosynthetic process	275
1.7738861739635468	4.7619	5	growth	95
1.7727066993713378	2.4510	6	regulation of protein kinase activity	236
	2.3810		regulation of kinase activity	243
	2.3364		regulation of transferase activity	247
1.769944667816162	14.2857	1	myoblast fusion	8
1.765833854675293	20.0000	2	antigen processing and presentation of endogenous peptide antigen	12
			antigen processing and presentation of endogenous peptide antigen via MHC class I
	16.6667		antigen processing and presentation of endogenous antigen	14
	12.5000	4	antigen processing and presentation of peptide antigen via MHC class I	31
	10.0000		antigen processing and presentation of peptide antigen	36
	2.7027	3	antigen processing and presentation	127
1.7584588527679443	50.0000	1	L-cystine transport	2
			sulfur amino acid transport
	7.6923		L-amino acid transport	13
1.7531960964202882	2.3364	6	mRNA processing	242
	1.9841		mRNA metabolic process	289
1.7502639293670654	6.2500	1	calcium-independent cell-cell adhesion	20
	4.1667		axon ensheathment	29
			ensheathment of neurons
1.7321138381958008	2.2222		meiosis	49
1.7273110449314117	1.3423	5	regulation of multicellular organismal process	353

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.