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

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	
6.564077854156494	5.5556	1	19	transcription from RNA polymerase III promoter	
5.84607458114624	20.0000	1	5	beta-tubulin folding	
5.84607458114624	14.2857	1	8	tubulin folding	
5.835443019866943	100.0000	1	1	oocyte differentiation	
5.835443019866943	50.0000	1	2	positive regulation of meiosis	
5.835443019866943	33.3333	1	3	regulation of meiosis	
5.835443019866943	10.0000	1	12	regulation of exit from mitosis	
5.835443019866943	6.2500	2	27	single fertilization	
5.835443019866943	5.5556	2	30	fertilization	
5.326116561889648	5.2632	1	22	cellular respiration	
5.326116561889648	1.4085	1	82	energy derivation by oxidation of organic compounds	
5.230461120605469	9.0909	1	13	phosphoinositide phosphorylation	
5.230461120605469	8.3333	1	14	lipid phosphorylation	
5.230461120605469	3.3333	1	35	lipid modification	
5.230461120605469	1.7857	1	76	phosphoinositide-mediated signaling	
5.197549819946289	11.1111	1	11	hormone-mediated signaling	
5.197549819946289	3.2258	1	32	fatty acid oxidation	
5.197549819946289	1.3158	1	85	response to hormone stimulus	
4.7113165855407715	1.9608	1	68	glycolysis	
4.7113165855407715	1.6393	1	79	glucose catabolic process	
4.7113165855407715	1.4706	1	89	hexose catabolic process	
4.7113165855407715	1.4493	1	90	monosaccharide catabolic process	
4.7113165855407715	1.3699	1	96	alcohol catabolic process	
4.7113165855407715	1.1236	1	114	cellular carbohydrate catabolic process	
4.7113165855407715	1.0638	1	121	carbohydrate catabolic process	
4.7113165855407715	0.9615	1	130	glucose metabolic process	
4.7113165855407715	0.6944	1	174	hexose metabolic process	
4.7113165855407715	0.6623	1	182	monosaccharide metabolic process	
4.620415210723877	2.7027	1	40	protein amino acid N-linked glycosylation	
4.601345539093018	1.0811	2	225	reproductive process	
4.506189823150635	5.8824	1	18	phagocytosis	
4.492823123931885	6.6667	1	20	negative regulation of gene expression, epigenetic	
4.492823123931885	2.2222	1	53	regulation of gene expression, epigenetic	
4.407965660095215	1.3333	1	100	neuropeptide signaling pathway	
4.105485280354817	5.4545	4	80	humoral immune response	
4.079947471618652	3.4483	1	32	insulin receptor signaling pathway	
4.046511650085449	50.0000	2	3	nuclear migration	
4.046511650085449	33.3333	1	3	nuclear membrane organization and biogenesis	
4.046511650085449	25.0000	2	6	establishment of nucleus localization	
4.046511650085449	12.5000	1	9	mitotic spindle organization and biogenesis	
4.037245273590088	14.2857	1	7	transmembrane receptor protein tyrosine phosphatase signaling pathway	
3.9217323064804077	40.0000	2	5	embryonic skeletal morphogenesis	
3.9217323064804077	18.1818	2	13	skeletal morphogenesis	
3.895843982696533	1.0309	1	109	Wnt receptor signaling pathway	
3.819567561149597	3.2258	4	133	regulation of cell growth	
3.8173599243164062	2.9412	1	39	transcription initiation from RNA polymerase II promoter	
3.8173599243164062	1.7857	1	68	transcription initiation	
3.721451759338379	4.4444	2	53	chromatin remodeling	
3.7029240131378174	50.0000	1	2	myoblast migration	
3.7029240131378174	11.1111	1	10	thymus development	

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/