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 1 to 14 of 14 in total

Would Be Affected (#genes)  : 10
Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class
4.7059	2.4113256633281708	216	response to freezing
4.6784		217	homoiothermy
4.4444		226	thermoregulation
2.9801	2.3975469536251492	338	positive regulation of transcription
2.9197	2.4850547462701797	358	response to wounding
2.8939	2.3975469536251492	347	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.5000	3.175950493131365	416	establishment and/or maintenance of chromatin architecture
2.4561		422	DNA packaging
2.2670	1.8413102626800537	448	RNA processing
2.0349	3.175950493131365	496	chromosome organization and biogenesis (sensu Eukaryota)
1.9824	2.121824940045675	510	vesicle-mediated transport
1.9737	1.6538901064130995	527	regulation of cell proliferation
1.8182	2.7119380235671997	531	cytoskeleton organization and biogenesis
1.7699	1.7068785279989243	545	cellular 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.