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	affected	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 Size (#genes)	Class	Class
2.5307	2.328269682611738	90	3555	protein metabolic process	biological process
2.5271	2.2348088707242693	8	321	nervous system development
	1.9810669592448644	26	1044	calcium ion binding	molecular function
2.5270	2.3636351216514155	208	8234	metabolic process	biological process
2.5172	1.6883443919095127	13	514	cell-cell signaling
2.5078	2.4881605356931686	9	370	cation channel activity	molecular function
	2.046714186668396			cell proliferation	biological process
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	nucleic acid binding	molecular function
2.4996	2.3858967367693675	181	7233	cellular metabolic process	biological 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	DNA binding	molecular function
2.4781	2.3607054107329426	20	810	establishment of protein localization	biological process
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
2.4502	2.0289560481905937	19	789	cation transporter activity	molecular function
2.4413	2.246480769722174	377	15431	biological_process	biological process
2.4400	2.241470267334763	319	13082	binding	molecular function
2.4356	2.2664323395275208	452	18539	all	universal
2.4354	2.2681225514251913	179	7366	protein binding	molecular function
2.4343	2.357159194284982	178	7318	primary metabolic process	biological process
2.4279	2.216642654982189	192	7902	intracellular organelle	cellular component
2.4275			7904	organelle
2.4272	2.0707096576690676	11	466	system development	biological process
2.4157	2.215940025315356	170	7030	intracellular membrane-bound organelle	cellular component
				membrane-bound organelle
2.4123	1.9621534997766668	25	1036	positive regulation of cellular process	biological process
2.4081	2.3038527108075324	66	2739	developmental process
2.4068	2.374769774137759	130	5408	macromolecule metabolic process
2.4064	2.6960288683573403	11	442	small GTPase mediated signal transduction
2.4047	2.248631090488074	73	3018	regulation of metabolic process
2.4030	2.2609615601026096	18	734	peptidase activity	molecular function
2.3959	2.1234114333987235	104	4348	regulation of cellular process	biological process
2.3936	1.6601282623079088	10	437	cytoskeletal protein binding	molecular function
2.3913	2.259431820927244	401	16757	molecular_function
2.3834	2.210925724557651	239	10046	intracellular part	cellular component
2.3831	2.2576280551010304	352	14761	cell part
2.3810	1.7727066993713378	6	243	regulation of kinase activity	biological process
2.3785	2.1435875109263827	96	4035	cation binding	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.