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

Results: HTML CSV LaTeX

Showing element 4309 to 4358 of 8866 in total

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

Class	Class Size (#genes)	Class
initiation of primordial ovarian follicle growth	1	biological process
innate immune response	78
innate immune response activating cell surface receptor signaling pathway	3
innate immune response-activating signal transduction	7
inner cell mass cell differentiation	2
inner cell mass cell proliferation	6
inner ear receptor cell differenation	13
inner ear receptor cell fate commitment	1
inner ear receptor stereocilium organization and biogenesis	6
inner kinetochore of condensed chromosome	2	cellular component
inner mitochondrial membrane organization and biogenesis	7	biological process
inorganic diphosphatase activity		molecular function
inorganic diphosphate transporter activity	1
inorganic phosphate transporter activity	3
inositol 1,3,4,5 tetrakisphosphate binding	2
inositol 1,4,5-triphosphate-sensitive calcium-release channel activity	6
inositol and derivative phosphorylation	2	biological process
inositol biosynthetic process	1
inositol bisphosphate phosphatase activity	2	molecular function
inositol catabolic process	1	biological process
inositol hexakisphosphate kinase activity	3	molecular function
inositol metabolic process	6	biological process
inositol or phosphatidylinositol phosphatase activity	38	molecular function
inositol or phosphatidylinositol phosphodiesterase activity	27
inositol oxygenase activity	1
inositol pentakisphosphate 2-kinase activity
inositol phosphate dephosphorylation		biological process
inositol phosphate-mediated signaling	4
inositol polyphosphate multikinase activity	1	molecular function
inositol tetrakisphosphate 1-kinase activity
inositol tetrakisphosphate kinase activity
inositol trisphosphate 3-kinase activity	7
inositol trisphosphate kinase activity
inositol trisphosphate phosphatase activity	6
inositol-1(or 4)-monophosphatase activity	4
inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity	1
inositol-1,4,5-triphosphate receptor activity	4
inositol-1,4-bisphosphate 1-phosphatase activity	1
inositol-3-phosphate synthase activity
inositol-polyphosphate 5-phosphatase activity	6
insemination	3	biological process
insoluble fraction	25	cellular component
insulin binding	2	molecular function
insulin processing	1	biological process
insulin receptor activity		molecular function
insulin receptor substrate binding	6
insulin secretion	11	biological process
insulin-like growth factor binding	24	molecular function
insulin-like growth factor binding protein complex	1	cellular component
insulin-like growth factor I binding		molecular function

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.