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	Microarray Measured (#genes)	affected	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	molecular function	sequence-specific DNA binding
3.4146	1.6467143297195435	8	229	biological process	cell cycle phase
3.4014	1.753389847278595	11	326	cellular component	cytoplasmic vesicle
3.3727	2.201178240776062	24	723	molecular function	hydrolase activity, acting on ester bonds
3.3626	1.8800545464391294	29	877		receptor binding
3.3557	1.753389847278595	11	331	cellular component	vesicle
3.3333	1.8456570080348425	8	249	molecular function	RNA polymerase II transcription factor activity
	1.3052469968795777	6	170	biological process	regulation of cell differentiation
3.2258	2.3798144817352296	12	378		alcohol metabolic process
3.1873	1.9443604201078415	9	295	molecular function	electrochemical potential-driven transporter activity
					porter activity
3.1746	1.8491697907447815	7	208	cellular component	synapse
3.1250	1.3853561878204346	6	197		vacuole
3.0968	2.4829982866843543	28	890	biological process	phosphate metabolic process
					phosphorus metabolic process
3.0928	2.506679137547811	10	331	molecular function	transcriptional activator activity
	2.506638288497925	7	238	cellular component	microtubule
3.0628	1.9421986639499664	25	807	molecular function	pyrophosphatase activity
3.0612	1.9925966064135234	7	216	cellular component	cytoplasmic membrane-bound vesicle
					membrane-bound vesicle
3.0581	1.9421986639499664	25	811	molecular function	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
3.0488			814		hydrolase activity, acting on acid anhydrides
3.0405	2.470501118236118	52	1721	biological process	protein modification process
3.0400	2.231512101073014	22	739	cellular component	membrane fraction
3.0351	1.9826314010118182	24	778	molecular function	nucleoside-triphosphatase activity
3.0303	1.8281174573031338	13	432		carrier activity
	1.6056334376335144	14	458	biological process	cell cycle
	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	cellular component	cell fraction
2.9070	2.844642996788025	6	206	biological process	nucleocytoplasmic transport
2.8939	2.3975469536251492	10	347		positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.8754	2.523834652370877		363	molecular function	identical protein binding
2.8736	2.530326783657074	12	416	biological process	response to abiotic stimulus
2.8672	2.005756884290461	73	2534	molecular function	hydrolase activity
2.8646	2.5862315134568648	13	443	biological process	ubiquitin cycle
2.8333	2.1418599311043236	19	686		anatomical structure morphogenesis
2.8249	2.7829527854919434	6	211		visual perception
2.8226	2.3674656118665425	45	1596	molecular function	transcription regulator activity
2.8112	1.6669044835226876	9	327		iron ion binding
2.8090	2.7829527854919434	6	212	biological process	sensory perception of light stimulus
2.7888	1.4970425537654333	9	311	molecular function	ATPase activity, coupled
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.