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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

% Affected Genes	Class	Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#genes)	Class
3.0351	molecular function	24	1.9826314010118182	778	nucleoside-triphosphatase activity
3.0303	biological process	7	1.3425244291623433	222	cell division
		14	1.6056334376335144	458	cell cycle
	molecular function	13	1.8281174573031338	432	carrier activity
3.0060	biological process	37	2.403050871690114	1226	response to stress
2.9801		10	2.3975469536251492	338	positive regulation of transcription
2.9680		15	2.46775693159837	499	regulation of transcription from RNA polymerase II promoter
2.9529		43	2.4479837675352356	1442	post-translational protein modification
2.9412		6	2.9956377029418944	195	chromatin modification
2.9393		52	2.470501118236118	1780	biopolymer modification
2.9289		9	2.6086528982434953	318	inflammatory response
2.9197		10	2.4850547462701797	358	response to wounding
2.9091	cellular component	28	2.266423319776853	972	cell fraction
2.9070	biological process	6	2.844642996788025	206	nucleocytoplasmic transport
2.8939		10	2.3975469536251492	347	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.8754	molecular function		2.523834652370877	363	identical protein binding
2.8736	biological process	12	2.530326783657074	416	response to abiotic stimulus
2.8672	molecular function	73	2.005756884290461	2534	hydrolase activity
2.8646	biological process	13	2.5862315134568648	443	ubiquitin cycle
2.8333		19	2.1418599311043236	686	anatomical structure morphogenesis
2.8249		6	2.7829527854919434	211	visual perception
2.8226	molecular function	45	2.3674656118665425	1596	transcription regulator activity
2.8112		9	1.6669044835226876	327	iron ion binding
2.8090	biological process	6	2.7829527854919434	212	sensory perception of light stimulus
2.7888	molecular function	9	1.4970425537654333	311	ATPase activity, coupled
2.7778			2.043148085474968	323	transcription cofactor activity
2.7661		57	2.1108567559200786	2054	purine nucleotide binding
2.7494	cellular component	70	2.1094915312389997	2528	intracellular
2.7174	biological process	6	3.0316067695617677	231	microtubule-based process
2.6820		33	2.7678764888218472	1217	intracellular signaling cascade
2.6684	molecular function	26	1.9353263832273937	960	ion transporter activity
2.6596	biological process	6	1.6556044340133667	229	anion transport
2.6465	cellular component	16	1.9401746136801583	591	Golgi apparatus
2.6362	biological process	42	2.630213709672292	1588	transcription
2.6247		11	2.28793443441391	429	positive regulation of cellular metabolic process
2.6245		69	2.3178554457061145	2628	regulation of transcription
2.6239	molecular function	12	2.134790725178189	476	endopeptidase activity
2.6235	biological process	20	2.3607054107329426	768	protein transport
2.6201		19	2.6820639967918396	735	immune response
2.6103		33	2.1811264465595115	1273	anatomical structure development
2.6042	molecular function	12	1.9343409657478332	442	transcription factor binding
2.6038	biological process	89	2.408202938131384	3425	biopolymer metabolic process
2.5907		70	2.2985232734680174	2698	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.5890		18	2.6417386531829834	711	phosphorylation
2.5757	cellular component	121	2.420156256183163	4692	nucleus
2.5654	molecular function	62	2.040321083068848	2412	nucleotide binding
2.5554	biological process	17	2.5815784772237143	675	protein amino acid phosphorylation
2.5487	cellular component	20	1.8778342920191147	770	endoplasmic reticulum
2.5375	biological process	62	2.3732517415826972	2448	regulation of transcription, DNA-dependent
2.5312		84	2.365392540051387	3325	cellular protein metabolic process

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.