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	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

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