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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8866 in total

% Affected Genes	Class	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
50.0000	female genitalia development	1.258076786994934	1	2	biological process
	glyoxylate cycle	1.1949561834335327
	GMP reductase activity	4.405977725982666			molecular function
	growth hormone-releasing hormone activity	1.1086714267730713
	interleukin-1 receptor complex	3.5441412925720215	2	3	cellular component
	interleukin-3 binding	1.1882063150405884	1	2	molecular function
	interleukin-3 receptor activity
	interleukin-5 binding
	interleukin-5 receptor activity
	isocitrate dehydrogenase (NADP+) activity	1.1949561834335327
	isocitrate metabolic process				biological process
	L-cystine transport	1.7584588527679443
	lamellar body	1.2250217199325562			cellular component
	myoblast migration	3.7029240131378174			biological process
	negative regulation of cardiac muscle cell proliferation	1.3346540927886963
	negative regulation of protein amino acid autophosphorylation	2.104278087615967
	nuclear migration	4.046511650085449	2	3
	oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor	4.405977725982666	1	2	molecular function
	palate development	1.258076786994934			biological process
	parathyroid hormone receptor activity	4.553711891174316			molecular function
	polydeoxyribonucleotide kinase activity	3.2158093452453613
	polynucleotide kinase activity
	positive regulation of cardioblast differentiation	1.3346540927886963			biological process
	positive regulation of growth hormone secretion	1.1086714267730713
	positive regulation of meiosis	5.835443019866943
	positive regulation of T-helper 2 cell differentiation	1.2514674663543701
	positive regulation of viral genome replication	3.367248058319092	2	3
	prostaglandin-endoperoxide synthase activity	1.1809606552124023	1	2	molecular function
	pyruvate kinase activity	4.7113165855407715
	regulation of antiviral response by host	3.367248058319092	2	4	biological process
	regulation of astrocyte differentiation	1.4955823421478271	1	2
	regulation of cardioblast differentiation	1.3346540927886963
	regulation of growth hormone secretion	1.1086714267730713
	regulation of protein amino acid autophosphorylation	2.104278087615967
	regulation of viral transcription	3.367248058319092	2	3
	response to sterol depletion	1.2384507656097412	1	2
	ribonuclease MRP complex	2.1270928382873535			cellular component
	sulfur amino acid transport	1.7584588527679443			biological process
	zygotic determination of anterior/posterior axis, embryo	1.1913443803787231
40.0000	embryonic skeletal morphogenesis	3.9217323064804077	2	5
33.3333	2-acylglycerol O-acyltransferase activity	3.313642740249634		6	molecular function
	alpha(1,2)-fucosyltransferase activity	1.2915130853652954	1	3
	apical junction complex	1.4628015756607056			cellular component
	arm morphogenesis	1.3346540927886963			biological process
	axon guidance receptor activity	3.485576868057251	2	6	molecular function
	beta-galactoside alpha-2,3-sialyltransferase activity	1.6965752840042114	1	3
	cullin-RING ubiquitin ligase complex	2.3310728073120117			cellular component
	cytokinesis during cell cycle	1.2983962297439575	2	6	biological process
	embryonic arm morphogenesis	1.3346540927886963	1	3
	establishment of mitotic spindle localization	1.2983962297439575

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.