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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

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

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.