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

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.