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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

% Affected Genes	Class	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)	Class
3.0351	molecular function	1.9826314010118182	778	24	nucleoside-triphosphatase activity
3.0303	biological process	1.6056334376335144	458	14	cell cycle
		1.3425244291623433	222	7	cell division
	molecular function	1.8281174573031338	432	13	carrier activity
3.0060	biological process	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	cellular component	2.266423319776853	972	28	cell fraction
2.9070	biological process	2.844642996788025	206	6	nucleocytoplasmic transport
2.8939		2.3975469536251492	347	10	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	2.530326783657074	416	12	response to abiotic stimulus
2.8672	molecular function	2.005756884290461	2534	73	hydrolase activity
2.8646	biological process	2.5862315134568648	443	13	ubiquitin cycle
2.8333		2.1418599311043236	686	19	anatomical structure morphogenesis
2.8249		2.7829527854919434	211	6	visual perception
2.8226	molecular function	2.3674656118665425	1596	45	transcription regulator activity
2.8112		1.6669044835226876	327	9	iron ion binding
2.8090	biological process	2.7829527854919434	212	6	sensory perception of light stimulus
2.7888	molecular function	1.4970425537654333	311	9	ATPase activity, coupled
2.7778		2.043148085474968	323		transcription cofactor activity
2.7661		2.1108567559200786	2054	57	purine nucleotide binding
2.7494	cellular component	2.1094915312389997	2528	70	intracellular
2.7174	biological process	3.0316067695617677	231	6	microtubule-based process
2.6820		2.7678764888218472	1217	33	intracellular signaling cascade
2.6684	molecular function	1.9353263832273937	960	26	ion transporter activity
2.6596	biological process	1.6556044340133667	229	6	anion transport
2.6465	cellular component	1.9401746136801583	591	16	Golgi apparatus
2.6362	biological process	2.630213709672292	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	molecular function	2.134790725178189	476	12	endopeptidase activity
2.6235	biological process	2.3607054107329426	768	20	protein transport
2.6201		2.6820639967918396	735	19	immune response
2.6103		2.1811264465595115	1273	33	anatomical structure development
2.6042	molecular function	1.9343409657478332	442	12	transcription factor binding
2.6038	biological process	2.408202938131384	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	cellular component	2.420156256183163	4692	121	nucleus
2.5654	molecular function	2.040321083068848	2412	62	nucleotide binding
2.5554	biological process	2.5815784772237143	675	17	protein amino acid phosphorylation
2.5487	cellular component	1.8778342920191147	770	20	endoplasmic reticulum
2.5375	biological process	2.3732517415826972	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.