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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Average Regulation (ratio)	Class	Class
3.4188	20	579	2.1927802711725235	sequence-specific DNA binding	molecular function
3.4146	8	229	1.6467143297195435	cell cycle phase	biological process
3.4014	11	326	1.753389847278595	cytoplasmic vesicle	cellular component
3.3727	24	723	2.201178240776062	hydrolase activity, acting on ester bonds	molecular function
3.3626	29	877	1.8800545464391294	receptor binding
3.3557	11	331	1.753389847278595	vesicle	cellular component
3.3333	6	170	1.3052469968795777	regulation of cell differentiation	biological process
	8	249	1.8456570080348425	RNA polymerase II transcription factor activity	molecular function
3.2258	12	378	2.3798144817352296	alcohol metabolic process	biological process
3.1873	9	295	1.9443604201078415	electrochemical potential-driven transporter activity	molecular function
				porter activity
3.1746	7	208	1.8491697907447815	synapse	cellular component
3.1250	6	197	1.3853561878204346	vacuole
3.0968	28	890	2.4829982866843543	phosphate metabolic process	biological process
				phosphorus metabolic process
3.0928	7	238	2.506638288497925	microtubule	cellular component
	10	331	2.506679137547811	transcriptional activator activity	molecular function
3.0628	25	807	1.9421986639499664	pyrophosphatase activity
3.0612	7	216	1.9925966064135234	cytoplasmic membrane-bound vesicle	cellular component
				membrane-bound vesicle
3.0581	25	811	1.9421986639499664	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	molecular function
3.0488		814		hydrolase activity, acting on acid anhydrides
3.0405	52	1721	2.470501118236118	protein modification process	biological process
3.0400	22	739	2.231512101073014	membrane fraction	cellular component
3.0351	24	778	1.9826314010118182	nucleoside-triphosphatase activity	molecular function
3.0303	7	222	1.3425244291623433	cell division	biological process
	13	432	1.8281174573031338	carrier activity	molecular function
	14	458	1.6056334376335144	cell cycle	biological process
3.0060	37	1226	2.403050871690114	response to stress
2.9801	10	338	2.3975469536251492	positive regulation of transcription
2.9680	15	499	2.46775693159837	regulation of transcription from RNA polymerase II promoter
2.9529	43	1442	2.4479837675352356	post-translational protein modification
2.9412	6	195	2.9956377029418944	chromatin modification
2.9393	52	1780	2.470501118236118	biopolymer modification
2.9289	9	318	2.6086528982434953	inflammatory response
2.9197	10	358	2.4850547462701797	response to wounding
2.9091	28	972	2.266423319776853	cell fraction	cellular component
2.9070	6	206	2.844642996788025	nucleocytoplasmic transport	biological process
2.8939	10	347	2.3975469536251492	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.8754		363	2.523834652370877	identical protein binding	molecular function
2.8736	12	416	2.530326783657074	response to abiotic stimulus	biological process
2.8672	73	2534	2.005756884290461	hydrolase activity	molecular function
2.8646	13	443	2.5862315134568648	ubiquitin cycle	biological process
2.8333	19	686	2.1418599311043236	anatomical structure morphogenesis
2.8249	6	211	2.7829527854919434	visual perception
2.8226	45	1596	2.3674656118665425	transcription regulator activity	molecular function
2.8112	9	327	1.6669044835226876	iron ion binding
2.8090	6	212	2.7829527854919434	sensory perception of light stimulus	biological process
2.7888	9	311	1.4970425537654333	ATPase activity, coupled	molecular function
2.7778		323	2.043148085474968	transcription cofactor activity

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.