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 101 to 150 of 328 in total

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
2.7661	2.1108567559200786	57	2054	molecular function	purine nucleotide binding
2.7494	2.1094915312389997	70	2528	cellular component	intracellular
2.7174	3.0316067695617677	6	231	biological process	microtubule-based process
2.6820	2.7678764888218472	33	1217		intracellular signaling cascade
2.6684	1.9353263832273937	26	960	molecular function	ion transporter activity
2.6596	1.6556044340133667	6	229	biological process	anion transport
2.6465	1.9401746136801583	16	591	cellular component	Golgi apparatus
2.6362	2.630213709672292	42	1588	biological process	transcription
2.6247	2.28793443441391	11	429		positive regulation of cellular metabolic process
2.6245	2.3178554457061145	69	2628		regulation of transcription
2.6239	2.134790725178189	12	476	molecular function	endopeptidase activity
2.6235	2.3607054107329426	20	768	biological process	protein transport
2.6201	2.6820639967918396	19	735		immune response
2.6103	2.1811264465595115	33	1273		anatomical structure development
2.6042	1.9343409657478332	12	442	molecular function	transcription factor binding
2.6038	2.408202938131384	89	3425	biological process	biopolymer metabolic process
2.5907	2.2985232734680174	70	2698		regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.5890	2.6417386531829834	18	711		phosphorylation
2.5757	2.420156256183163	121	4692	cellular component	nucleus
2.5654	2.040321083068848	62	2412	molecular function	nucleotide binding
2.5554	2.5815784772237143	17	675	biological process	protein amino acid phosphorylation
2.5487	1.8778342920191147	20	770	cellular component	endoplasmic reticulum
2.5375	2.3732517415826972	62	2448	biological process	regulation of transcription, DNA-dependent
2.5312	2.365392540051387	84	3325		cellular protein metabolic process
2.5307	2.328269682611738	90	3555		protein metabolic process
2.5271	2.2348088707242693	8	321		nervous system development
	1.9810669592448644	26	1044	molecular function	calcium ion binding
2.5270	2.3636351216514155	208	8234	biological process	metabolic process
2.5172	1.6883443919095127	13	514		cell-cell signaling
2.5078	2.4881605356931686	9	370	molecular function	cation channel activity
	2.046714186668396			biological process	cell proliferation
2.5057	2.319896697998047	13	534		intracellular protein transport
2.5048	2.0103142169805674	16	623		homeostatic process
2.5045	2.539123611790793		644		organ development
2.5000	3.175950493131365	10	416		establishment and/or maintenance of chromatin architecture
	2.2792132452352725	96	3858	molecular function	nucleic acid binding
2.4996	2.3858967367693675	181	7233	biological process	cellular metabolic process
2.4922	2.8815125972032547	9	379		apoptosis
2.4857	2.365392540051387	84	3377		cellular macromolecule metabolic process
2.4845	2.8815125972032547	9	381		programmed cell death
2.4798	2.3028621958649675	65	2641	molecular function	DNA binding
2.4781	2.3607054107329426	20	810	biological process	establishment of protein localization
2.4658	2.8162122435039945	11	430		cell death
					death
2.4655	2.017735466957092	29	1165		positive regulation of biological process
2.4631	2.28793443441391	11	456		positive regulation of metabolic process
2.4610	2.2670372059712043	72	2913		regulation of cellular metabolic process
2.4561	3.175950493131365	10	422		DNA packaging
2.4522	2.252760338363143	294	11986		cellular process
2.4510	1.7727066993713378	6	236		regulation of protein kinase 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.