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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 101 to 150 of 328 in total

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Would Be Affected (#genes)	Class	Class
2.7661	2.1108567559200786	2054	57	molecular function	purine nucleotide binding
2.7494	2.1094915312389997	2528	70	cellular component	intracellular
2.7174	3.0316067695617677	231	6	biological process	microtubule-based process
2.6820	2.7678764888218472	1217	33		intracellular signaling cascade
2.6684	1.9353263832273937	960	26	molecular function	ion transporter activity
2.6596	1.6556044340133667	229	6	biological process	anion transport
2.6465	1.9401746136801583	591	16	cellular component	Golgi apparatus
2.6362	2.630213709672292	1588	42	biological process	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	476	12	molecular function	endopeptidase activity
2.6235	2.3607054107329426	768	20	biological process	protein transport
2.6201	2.6820639967918396	735	19		immune response
2.6103	2.1811264465595115	1273	33		anatomical structure development
2.6042	1.9343409657478332	442	12	molecular function	transcription factor binding
2.6038	2.408202938131384	3425	89	biological process	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	4692	121	cellular component	nucleus
2.5654	2.040321083068848	2412	62	molecular function	nucleotide binding
2.5554	2.5815784772237143	675	17	biological process	protein amino acid phosphorylation
2.5487	1.8778342920191147	770	20	cellular component	endoplasmic reticulum
2.5375	2.3732517415826972	2448	62	biological process	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
	1.9810669592448644	1044	26	molecular function	calcium ion binding
2.5270	2.3636351216514155	8234	208	biological process	metabolic process
2.5172	1.6883443919095127	514	13		cell-cell signaling
2.5078	2.4881605356931686	370	9	molecular function	cation channel activity
	2.046714186668396			biological process	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
	2.2792132452352725	3858	96	molecular function	nucleic acid binding
2.4996	2.3858967367693675	7233	181	biological process	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
2.4798	2.3028621958649675	2641	65	molecular function	DNA binding
2.4781	2.3607054107329426	810	20	biological process	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
2.4610	2.2670372059712043	2913	72		regulation of cellular metabolic process
2.4561	3.175950493131365	422	10		DNA packaging
2.4522	2.252760338363143	11986	294		cellular process
2.4510	1.7727066993713378	236	6		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.