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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 10 of 10 in total

Would Be Affected (#genes)  : 20

Class Size (#genes)	Average Regulation (ratio)	Class	% Affected Genes	Class
579	2.1927802711725235	sequence-specific DNA binding	3.4188	molecular function
768	2.3607054107329426	protein transport	2.6235	biological process
770	1.8778342920191147	endoplasmic reticulum	2.5487	cellular component
810	2.3607054107329426	establishment of protein localization	2.4781	biological process
879	2.6115847550905666	immune system process	2.2184
914	2.1725611826952766	establishment of cellular localization	2.2398
938	2.718373046201818	kinase activity	2.1277	molecular function
955	2.4005173126856487	oxidoreductase activity	2.0492
1060	2.299432896077633	integral to plasma membrane	1.8561	cellular component
1077		intrinsic to plasma membrane	1.8286

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.