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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 328 in total

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