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

Results: HTML CSV LaTeX

Showing element 4909 to 4958 of 8866 in total

Average Regulation (ratio)  : no value
% Affected Genes  : no value
Would Be Affected (#genes)  : no value
Class Size (#genes)  : 2

Class	Class
positive regulation of urothelial cell proliferation	biological process
positive regulation of viral transcription
post-chaperonin tubulin folding pathway
posterior midgut development
prenylated protein catabolic process
prenylated protein tyrosine phosphatase activity	molecular function
prepulse inhibition	biological process
preribosome	cellular component
primary lysosome
primary sex determination	biological process
processing of 20S pre-rRNA
prolactin receptor binding	molecular function
propionyl-CoA carboxylase activity
prostaglandin J receptor activity
prostaglandin-D synthase activity
protein amino acid dealkylation	biological process
protein amino acid demethylation
protein amino acid esterification
protein amino acid farnesylation
protein amino acid myristoylation
protein anchor	molecular function
protein carrier activity
protein channel activity
protein deglycosylation	biological process
protein desumoylation
protein farnesyltransferase activity	molecular function
protein heterotetramerization	biological process
protein insertion into mitochondrial membrane during induction of apoptosis
protein kinase B binding	molecular function
protein myristoylation	biological process
protein targeting to Golgi
protein tyrosine phosphatase activator activity	molecular function
protein xylosyltransferase activity
protein-arginine omega-N monomethyltransferase activity
protein-cysteine S-acyltransferase activity
protein-cysteine S-palmitoleyltransferase activity
protein-tyrosine sulfotransferase activity
proteoglycan binding
proteoglycan sulfotransferase activity
prothoracicotrophic hormone activity
PTB domain binding
purine base salvage	biological process
purine binding	molecular function
purine deoxyribonucleotide metabolic process	biological process
purine nucleoside biosynthetic process
purine nucleoside diphosphate biosynthetic process
purine nucleoside transporter activity	molecular function
purine nucleotide transport	biological process
purine ribonucleoside biosynthetic process
purine ribonucleoside diphosphate biosynthetic 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.