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	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 425 to 474 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
4.1667	1.6198676824569702	1	27	protein kinase C activation
	1.6074604988098145		30	response to antibiotic
	1.5287119547526042	3	74	amine transport
	1.3346540927886963	1	25	negative regulation of locomotion
	1.3014217615127563		28	positive regulation of amino acid metabolic process
				positive regulation of phosphorylation
				positive regulation of protein amino acid phosphorylation
	1.2915130853652954		24	regulation of microtubule polymerization or depolymerization
	1.20618736743927		26	sperm motility
	1.1954466104507446			DNA catabolic process
	1.1848907470703125		25	cyclic nucleotide biosynthetic process
4.0816	1.4733972549438477	2	54	blood pressure regulation
4.0000	2.104278087615967	1	28	epithelial cell differentiation
	1.5580885410308838		27	phosphoinositide biosynthetic process
	1.4955823421478271			regulation of ossification
	1.3599663376808167	2	58	MAPKKK cascade
	1.3014217615127563	1	29	positive regulation of phosphate metabolic process
	1.258076786994934			camera-type eye development
3.9773	2.6829177481787547	8	192	regulation of growth
3.9735	2.267966568470001	7	164	transmembrane receptor protein tyrosine kinase signaling pathway
3.9216	1.6685125231742859	2	58	sphingolipid metabolic process
	1.2790873646736145		57	gland development
3.8462	3.367248058319092	1	30	viral reproductive process
	2.6506848335266113	2	41	activation of plasma proteins during acute inflammatory response
				complement activation
	2.27594193816185	5	124	protein amino acid glycosylation
	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

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.