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 [...,...].

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 101 to 150 of 5007 in total

Class  : biological process

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
3.175950493131365	2.4561	10	422	DNA packaging
	2.0349		496	chromosome organization and biogenesis (sensu Eukaryota)
3.1701605319976807	13.3333	2	17	nuclear organization and biogenesis
3.1123706102371216	1.6260	3	209	response to other organism
3.0782742261886598	2.2026	15	680	defense response
3.0503673553466797	20.0000	1	5	substrate-bound cell migration, cell extension
	1.8519		60	cell projection biogenesis
	1.1765		94	cell projection organization and biogenesis
	0.9259		120	cell morphogenesis
3.0427030324935913	3.7736	2	64	dicarboxylic acid transport
3.0316067695617677	2.7174	6	231	microtubule-based process
2.9956377029418944	2.9412		195	chromatin modification
2.9439388116200766	1.5385	4	237	negative regulation of apoptosis
	1.5152		240	negative regulation of programmed cell death
2.941256210207939	2.1858	11	519	chromosome organization and biogenesis
2.938953399658203	6.2500	1	20	I-kappaB kinase/NF-kappaB cascade
2.9275668263435364	1.9417	2	119	skeletal development
2.9041290283203125	1.3423		162	endocytosis
	1.2903		168	membrane invagination
2.8815125972032547	2.4922	9	379	apoptosis
	2.4845		381	programmed cell death
2.8703815937042236	16.6667	1	8	sarcomere organization
	12.5000		9	response to calcium ion
2.8696537017822266	3.2258		33	DNA topological change
2.8630340496699014	3.3708	3	98	embryonic development
2.8629825115203857	1.2987	1	91	brain development
2.844642996788025	2.9070	6	206	nucleocytoplasmic transport
2.8162122435039945	2.4658	11	430	cell death
				death
2.812885562578837	1.4706	4	266	protein folding
2.8056000471115112	2.3669		186	positive regulation of transcription from RNA polymerase II promoter
	1.6260		276	positive regulation of transcription, DNA-dependent
2.7880274454752603	3.5714	3	95	G-protein signaling, coupled to cyclic nucleotide second messenger
	3.3333		101	cyclic-nucleotide-mediated signaling
2.7829527854919434	2.8249	6	211	visual perception
	2.8090		212	sensory perception of light stimulus
2.775389830271403	1.4151	5	344	sensory perception of smell
	1.3158		378	sensory perception of chemical stimulus
2.7678764888218472	2.6820	33	1217	intracellular signaling cascade
2.7504823207855225	100.0000	2	2	spindle assembly
	20.0000	1	5	centrosome duplication
	6.2500		17	centrosome organization and biogenesis
				microtubule organizing center organization and biogenesis
2.7469783226648965	10.7143	4	35	glycerol metabolic process
	10.3448		37	polyol metabolic process
2.745920252799988	1.1390	6	544	carbohydrate metabolic process
2.736812561750412	2.8777	5	165	negative regulation of transcription from RNA polymerase II promoter
	1.9900		238	negative regulation of transcription, DNA-dependent
2.7119380235671997	1.8182	10	531	cytoskeleton organization and biogenesis
2.7088398138682046	1.9481	5	265	protein-DNA complex assembly

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.