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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

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

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.