Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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) Class % Affected Genes Would Be Affected (#genes) affected Class Size (#genes) Class Microarray Measured (#genes) Accession
Results: HTML CSV LaTeX Showing element 1 to 50 of 5007 in total 
Class	biological process

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	
6.564077854156494	transcription from RNA polymerase III promoter	5.5556	1	19	
5.84607458114624	beta-tubulin folding	20.0000	1	5	
5.84607458114624	tubulin folding	14.2857	1	8	
5.835443019866943	fertilization	5.5556	2	30	
5.835443019866943	oocyte differentiation	100.0000	1	1	
5.835443019866943	positive regulation of meiosis	50.0000	1	2	
5.835443019866943	regulation of exit from mitosis	10.0000	1	12	
5.835443019866943	regulation of meiosis	33.3333	1	3	
5.835443019866943	single fertilization	6.2500	2	27	
5.326116561889648	cellular respiration	5.2632	1	22	
5.326116561889648	energy derivation by oxidation of organic compounds	1.4085	1	82	
5.230461120605469	lipid modification	3.3333	1	35	
5.230461120605469	lipid phosphorylation	8.3333	1	14	
5.230461120605469	phosphoinositide phosphorylation	9.0909	1	13	
5.230461120605469	phosphoinositide-mediated signaling	1.7857	1	76	
5.197549819946289	fatty acid oxidation	3.2258	1	32	
5.197549819946289	hormone-mediated signaling	11.1111	1	11	
5.197549819946289	response to hormone stimulus	1.3158	1	85	
4.7113165855407715	alcohol catabolic process	1.3699	1	96	
4.7113165855407715	carbohydrate catabolic process	1.0638	1	121	
4.7113165855407715	cellular carbohydrate catabolic process	1.1236	1	114	
4.7113165855407715	glucose catabolic process	1.6393	1	79	
4.7113165855407715	glucose metabolic process	0.9615	1	130	
4.7113165855407715	glycolysis	1.9608	1	68	
4.7113165855407715	hexose catabolic process	1.4706	1	89	
4.7113165855407715	hexose metabolic process	0.6944	1	174	
4.7113165855407715	monosaccharide catabolic process	1.4493	1	90	
4.7113165855407715	monosaccharide metabolic process	0.6623	1	182	
4.620415210723877	protein amino acid N-linked glycosylation	2.7027	1	40	
4.601345539093018	reproductive process	1.0811	2	225	
4.506189823150635	phagocytosis	5.8824	1	18	
4.492823123931885	negative regulation of gene expression, epigenetic	6.6667	1	20	
4.492823123931885	regulation of gene expression, epigenetic	2.2222	1	53	
4.407965660095215	neuropeptide signaling pathway	1.3333	1	100	
4.105485280354817	humoral immune response	5.4545	4	80	
4.079947471618652	insulin receptor signaling pathway	3.4483	1	32	
4.046511650085449	establishment of nucleus localization	25.0000	2	6	
4.046511650085449	mitotic spindle organization and biogenesis	12.5000	1	9	
4.046511650085449	nuclear membrane organization and biogenesis	33.3333	1	3	
4.046511650085449	nuclear migration	50.0000	2	3	
4.037245273590088	transmembrane receptor protein tyrosine phosphatase signaling pathway	14.2857	1	7	
3.9217323064804077	embryonic skeletal morphogenesis	40.0000	2	5	
3.9217323064804077	skeletal morphogenesis	18.1818	2	13	
3.895843982696533	Wnt receptor signaling pathway	1.0309	1	109	
3.819567561149597	regulation of cell growth	3.2258	4	133	
3.8173599243164062	transcription initiation	1.7857	1	68	
3.8173599243164062	transcription initiation from RNA polymerase II promoter	2.9412	1	39	
3.721451759338379	chromatin remodeling	4.4444	2	53	
3.7029240131378174	hemopoietic or lymphoid organ development	1.9608	1	66	
3.7029240131378174	myoblast migration	50.0000	1	2	

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.
- http://analysis.yellowcouch.org/