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 affected Would Be Affected (#genes) Class Size (#genes) Class Microarray Measured (#genes) Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 5007 in total

Class	biological process

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	
3.7029240131378174	striated muscle development	2.7778	1	38	
3.7029240131378174	thymus development	11.1111	1	10	
3.595149040222168	negative regulation of cell growth	7.6923	3	41	
3.595149040222168	negative regulation of growth	5.8824	3	57	
3.594250440597534	cell migration	0.9259	2	248	
3.575074315071106	axonogenesis	4.4444	2	49	
3.575074315071106	cell part morphogenesis	3.7736	2	59	
3.575074315071106	cell projection morphogenesis	3.7736	2	59	
3.575074315071106	neurite morphogenesis	3.7736	2	59	
3.485576868057251	axon guidance	1.4286	1	80	
3.4853661954402924	microtubule cytoskeleton organization and biogenesis	5.2632	5	87	
3.400171995162964	cellular structure morphogenesis	1.8987	3	176	
3.3986358642578125	second-messenger-mediated signaling	2.4691	5	201	
3.398496985435486	spindle organization and biogenesis	10.0000	2	23	
3.3942748308181763	glycerophospholipid metabolic process	3.1746	2	72	
3.3942748308181763	phosphoinositide metabolic process	4.3478	2	52	
3.3942748308181763	phospholipid metabolic process	1.5038	2	155	
3.367248058319092	interaction with host	5.5556	1	18	
3.367248058319092	interspecies interaction between organisms	2.1277	1	56	
3.367248058319092	multi-organism process	0.9346	1	131	
3.367248058319092	negative regulation of antiviral response	100.0000	1	1	
3.367248058319092	negative regulation of antiviral response by host	100.0000	1	1	
3.367248058319092	positive regulation of viral genome replication	50.0000	2	3	
3.367248058319092	positive regulation of viral life cycle	33.3333	2	5	
3.367248058319092	positive regulation of viral protein levels in host cell	100.0000	1	1	
3.367248058319092	regulation of antiviral response	33.3333	2	5	
3.367248058319092	regulation of antiviral response by host	50.0000	2	4	
3.367248058319092	regulation of viral genome replication	20.0000	2	10	
3.367248058319092	regulation of viral life cycle	11.1111	2	15	
3.367248058319092	regulation of viral protein levels in host cell	100.0000	1	1	
3.367248058319092	regulation of viral transcription	50.0000	2	3	
3.367248058319092	symbiosis, encompassing mutualism through parasitism	2.1277	1	56	
3.367248058319092	viral reproductive process	3.8462	1	30	
3.367248058319092	virus-host interaction	14.2857	1	7	
3.313642740249634	acylglycerol biosynthetic process	16.6667	1	7	
3.313642740249634	acylglycerol metabolic process	5.0000	1	28	
3.313642740249634	glycerol ether biosynthetic process	14.2857	1	8	
3.313642740249634	glycerol ether metabolic process	4.5455	1	30	
3.313642740249634	glycerolipid biosynthetic process	14.2857	1	8	
3.313642740249634	glycerolipid metabolic process	4.7619	1	29	
3.313642740249634	neutral lipid biosynthetic process	16.6667	1	7	
3.313642740249634	neutral lipid metabolic process	5.0000	1	28	
3.313642740249634	triacylglycerol biosynthetic process	25.0000	1	4	
3.313642740249634	triacylglycerol metabolic process	5.8824	1	23	
3.290644884109497	liver development	7.1429	1	15	
3.284923235575358	membrane organization and biogenesis	1.2876	3	252	
3.2791879177093506	response to pain	12.5000	1	8	
3.2791879177093506	sensory perception of pain	9.0909	1	11	
3.1892552375793457	fatty acid metabolic process	1.3072	2	172	
3.175950493131365	chromosome organization and biogenesis (sensu Eukaryota)	2.0349	10	496	

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/