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	affected	Class Size (#genes)	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

% Affected Genes	Average Regulation (ratio)	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
2.5307	2.328269682611738	90	protein metabolic process	3555	biological process
2.5271	2.2348088707242693	8	nervous system development	321
	1.9810669592448644	26	calcium ion binding	1044	molecular function
2.5270	2.3636351216514155	208	metabolic process	8234	biological process
2.5172	1.6883443919095127	13	cell-cell signaling	514
2.5078	2.4881605356931686	9	cation channel activity	370	molecular function
	2.046714186668396		cell proliferation		biological process
2.5057	2.319896697998047	13	intracellular protein transport	534
2.5048	2.0103142169805674	16	homeostatic process	623
2.5045	2.539123611790793		organ development	644
2.5000	3.175950493131365	10	establishment and/or maintenance of chromatin architecture	416
	2.2792132452352725	96	nucleic acid binding	3858	molecular function
2.4996	2.3858967367693675	181	cellular metabolic process	7233	biological process
2.4922	2.8815125972032547	9	apoptosis	379
2.4857	2.365392540051387	84	cellular macromolecule metabolic process	3377
2.4845	2.8815125972032547	9	programmed cell death	381
2.4798	2.3028621958649675	65	DNA binding	2641	molecular function
2.4781	2.3607054107329426	20	establishment of protein localization	810	biological process
2.4658	2.8162122435039945	11	cell death	430
			death
2.4655	2.017735466957092	29	positive regulation of biological process	1165
2.4631	2.28793443441391	11	positive regulation of metabolic process	456
2.4610	2.2670372059712043	72	regulation of cellular metabolic process	2913
2.4561	3.175950493131365	10	DNA packaging	422
2.4522	2.252760338363143	294	cellular process	11986
2.4510	1.7727066993713378	6	regulation of protein kinase activity	236
2.4502	2.0289560481905937	19	cation transporter activity	789	molecular function
2.4413	2.246480769722174	377	biological_process	15431	biological process
2.4400	2.241470267334763	319	binding	13082	molecular function
2.4356	2.2664323395275208	452	all	18539	universal
2.4354	2.2681225514251913	179	protein binding	7366	molecular function
2.4343	2.357159194284982	178	primary metabolic process	7318	biological process
2.4279	2.216642654982189	192	intracellular organelle	7902	cellular component
2.4275			organelle	7904
2.4272	2.0707096576690676	11	system development	466	biological process
2.4157	2.215940025315356	170	intracellular membrane-bound organelle	7030	cellular component
			membrane-bound organelle
2.4123	1.9621534997766668	25	positive regulation of cellular process	1036	biological process
2.4081	2.3038527108075324	66	developmental process	2739
2.4068	2.374769774137759	130	macromolecule metabolic process	5408
2.4064	2.6960288683573403	11	small GTPase mediated signal transduction	442
2.4047	2.248631090488074	73	regulation of metabolic process	3018
2.4030	2.2609615601026096	18	peptidase activity	734	molecular function
2.3959	2.1234114333987235	104	regulation of cellular process	4348	biological process
2.3936	1.6601282623079088	10	cytoskeletal protein binding	437	molecular function
2.3913	2.259431820927244	401	molecular_function	16757
2.3834	2.210925724557651	239	intracellular part	10046	cellular component
2.3831	2.2576280551010304	352	cell part	14761
2.3810	1.7727066993713378	6	regulation of kinase activity	243	biological process
2.3785	2.1435875109263827	96	cation binding	4035	molecular function

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.