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

Results: HTML CSV LaTeX

Showing element 25 to 74 of 173 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)	Class
3.0303	1.6056334376335144	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
2.9070	2.844642996788025	206	6	nucleocytoplasmic transport
2.8939	2.3975469536251492	347	10	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.8736	2.530326783657074	416	12	response to abiotic stimulus
2.8646	2.5862315134568648	443	13	ubiquitin cycle
2.8333	2.1418599311043236	686	19	anatomical structure morphogenesis
2.8249	2.7829527854919434	211	6	visual perception
2.8090		212		sensory perception of light stimulus
2.7174	3.0316067695617677	231		microtubule-based process
2.6820	2.7678764888218472	1217	33	intracellular signaling cascade
2.6596	1.6556044340133667	229	6	anion transport
2.6362	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
2.6235	2.3607054107329426	768	20	protein transport
2.6201	2.6820639967918396	735	19	immune response
2.6103	2.1811264465595115	1273	33	anatomical structure development
2.6038	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
2.5554	2.5815784772237143	675	17	protein amino acid phosphorylation
2.5375	2.3732517415826972	2448	62	regulation of transcription, DNA-dependent
2.5312	2.365392540051387	3325	84	cellular protein metabolic process
2.5307	2.328269682611738	3555	90	protein metabolic process
2.5271	2.2348088707242693	321	8	nervous system development
2.5270	2.3636351216514155	8234	208	metabolic process
2.5172	1.6883443919095127	514	13	cell-cell signaling
2.5078	2.046714186668396	370	9	cell proliferation
2.5057	2.319896697998047	534	13	intracellular protein transport
2.5048	2.0103142169805674	623	16	homeostatic process
2.5045	2.539123611790793	644		organ development
2.5000	3.175950493131365	416	10	establishment and/or maintenance of chromatin architecture
2.4996	2.3858967367693675	7233	181	cellular metabolic process
2.4922	2.8815125972032547	379	9	apoptosis
2.4857	2.365392540051387	3377	84	cellular macromolecule metabolic process
2.4845	2.8815125972032547	381	9	programmed cell death
2.4781	2.3607054107329426	810	20	establishment of protein localization
2.4658	2.8162122435039945	430	11	cell death
				death
2.4655	2.017735466957092	1165	29	positive regulation of biological process
2.4631	2.28793443441391	456	11	positive regulation of 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.