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	affected	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 501 to 550 of 5007 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class
3.3898	2.0335476994514465	2	65	cellular protein complex assembly
	1.9050463438034058			rRNA metabolic process
	1.7028499245643616		69	regulation of phosphorylation
3.3708	2.8630340496699014	3	98	embryonic development
3.3333	5.230461120605469	1	35	lipid modification
	2.7880274454752603	3	101	cyclic-nucleotide-mediated signaling
	1.9514372944831848	2	73	vitamin metabolic process
	1.9051852226257324		68	cAMP-mediated signaling
	1.4955823421478271	1	32	regulation of bone remodeling
	1.3052469968795777	6	170	regulation of cell differentiation
	1.3020682334899902	1	31	regulation of binding
	1.258076786994934		34	eye development
	1.1951740384101868	2	72	sulfur metabolic process
	1.1151909828186035	1	37	translational initiation
3.2967	1.9009546041488647	3	99	response to drug
3.2787	1.581991195678711	2	62	amino acid transport
	1.545079529285431		72	regulation of secretion
3.2520	1.9630463421344757	5	139	oxygen and reactive oxygen species metabolic process
3.2258	5.197549819946289	1	32	fatty acid oxidation
	3.819567561149597	4	133	regulation of cell growth
	2.8696537017822266	1	33	DNA topological change
	2.3798144817352296	12	378	alcohol metabolic process
	1.9489291310310364	4	138	sensory perception of sound
	1.3642695546150208	2	68	elevation of cytosolic calcium ion concentration
	1.2835599184036255	1	36	cell fate determination
	1.258076786994934			sensory organ development
	1.192122220993042		43	hormone biosynthetic process
3.2000	1.9489291310310364	4	139	sensory perception of mechanical stimulus
3.1746	3.3942748308181763	2	72	glycerophospholipid metabolic process
	1.7028499245643616		73	regulation of phosphate metabolic process
				regulation of phosphorus metabolic process
	1.3642695546150208		69	cytosolic calcium ion homeostasis
3.1250	1.4955823421478271	1	36	odontogenesis
	1.4563519954681396		32	DNA integrity checkpoint
	1.2915130853652954		37	establishment and/or maintenance of cell polarity
	1.2048066854476929		34	menstrual cycle process
	1.1848907470703125			cyclic nucleotide metabolic process
3.0968	2.4829982866843543	28	890	phosphate metabolic process
				phosphorus metabolic process
3.0405	2.470501118236118	52	1721	protein modification process
3.0303	1.9220449527104695	4	120	positive regulation of multicellular organismal process
	1.6198676824569702	1	38	caspase activation
			42	regulation of muscle contraction
	1.6056334376335144	14	458	cell cycle
	1.3425244291623433	7	222	cell division
	1.2733992338180542	1	36	regulated secretory pathway
	1.1882063150405884		41	cytokine and chemokine mediated signaling pathway
3.0060	2.403050871690114	37	1226	response to stress
3.0000	1.67010498046875	3	114	Golgi vesicle transport
2.9801	2.3975469536251492	10	338	positive regulation of transcription

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.