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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8866 in total

% Affected Genes	Average Regulation (ratio)	Class	Would Be Affected (#genes)	Class Size (#genes)	Class
50.0000	3.5441412925720215	interleukin-1 receptor complex	2	3	cellular component
	3.367248058319092	positive regulation of viral genome replication			biological process
		regulation of antiviral response by host		4
		regulation of viral transcription		3
	3.313642740249634	diacylglycerol O-acyltransferase activity	3	5	molecular function
	3.2158093452453613	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	1	2
		ATP-dependent polynucleotide kinase activity
		polydeoxyribonucleotide kinase activity
		polynucleotide kinase activity
	2.8086023926734924	aldehyde dehydrogenase [NAD(P)+] activity	3	6
	2.1270928382873535	ribonuclease MRP complex	1	2	cellular component
	2.104278087615967	negative regulation of protein amino acid autophosphorylation			biological process
		regulation of protein amino acid autophosphorylation
	1.7584588527679443	L-cystine transport
		sulfur amino acid transport
	1.4955823421478271	regulation of astrocyte differentiation
	1.3346540927886963	negative regulation of cardiac muscle cell proliferation
		positive regulation of cardioblast differentiation
		regulation of cardioblast differentiation
	1.2983962297439575	cytokinesis after mitosis	3	5
	1.258076786994934	female genitalia development	1	2
		palate development
	1.2514674663543701	positive regulation of T-helper 2 cell differentiation
	1.2384507656097412	response to sterol depletion
	1.2250217199325562	lamellar body			cellular component
	1.1954466104507446	deoxyribonuclease II activity			molecular function
		endodeoxyribonuclease activity, producing 3'-phosphomonoesters
	1.1949561834335327	glyoxylate cycle			biological process
		isocitrate dehydrogenase (NADP+) activity			molecular function
		isocitrate metabolic process			biological process
	1.1913443803787231	zygotic determination of anterior/posterior axis, embryo
	1.1882063150405884	interleukin-3 binding			molecular function
		interleukin-3 receptor activity
		interleukin-5 binding
		interleukin-5 receptor activity
	1.1809606552124023	prostaglandin-endoperoxide synthase activity
	1.1086714267730713	growth hormone-releasing hormone activity
		positive regulation of growth hormone secretion			biological process
		regulation of growth hormone secretion
40.0000	3.9217323064804077	embryonic skeletal morphogenesis	2	5
33.3333	5.835443019866943	regulation of meiosis	1	3
	4.046511650085449	nuclear chromosome, telomeric region			cellular component
		nuclear membrane organization and biogenesis			biological process
	3.5441412925720215	Toll binding			molecular function
	3.485576868057251	axon guidance receptor activity	2	6
	3.397643566131592	junctional membrane complex	1	3	cellular component
	3.367248058319092	positive regulation of viral life cycle	2	5	biological process
		regulation of antiviral response
	3.313642740249634	2-acylglycerol O-acyltransferase activity		6	molecular function
	2.5450799465179443	intercellular junction maintenance	1	3	biological 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.