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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

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