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)	Class	Would Be Affected (#genes)	Class	Microarray Measured (#genes)	Accession	affected

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Would Be Affected (#genes)	Class
2.5307	2.328269682611738	3555	biological process	90	protein metabolic process
2.5271	2.2348088707242693	321		8	nervous system development
	1.9810669592448644	1044	molecular function	26	calcium ion binding
2.5270	2.3636351216514155	8234	biological process	208	metabolic process
2.5172	1.6883443919095127	514		13	cell-cell signaling
2.5078	2.4881605356931686	370	molecular function	9	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	molecular function	96	nucleic acid binding
2.4996	2.3858967367693675	7233	biological process	181	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	molecular function	65	DNA binding
2.4781	2.3607054107329426	810	biological process	20	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
2.4502	2.0289560481905937	789	molecular function	19	cation transporter activity
2.4413	2.246480769722174	15431	biological process	377	biological_process
2.4400	2.241470267334763	13082	molecular function	319	binding
2.4356	2.2664323395275208	18539	universal	452	all
2.4354	2.2681225514251913	7366	molecular function	179	protein binding
2.4343	2.357159194284982	7318	biological process	178	primary metabolic process
2.4279	2.216642654982189	7902	cellular component	192	intracellular organelle
2.4275		7904			organelle
2.4272	2.0707096576690676	466	biological process	11	system development
2.4157	2.215940025315356	7030	cellular component	170	intracellular membrane-bound organelle
					membrane-bound organelle
2.4123	1.9621534997766668	1036	biological process	25	positive regulation of cellular process
2.4081	2.3038527108075324	2739		66	developmental process
2.4068	2.374769774137759	5408		130	macromolecule metabolic process
2.4064	2.6960288683573403	442		11	small GTPase mediated signal transduction
2.4047	2.248631090488074	3018		73	regulation of metabolic process
2.4030	2.2609615601026096	734	molecular function	18	peptidase activity
2.3959	2.1234114333987235	4348	biological process	104	regulation of cellular process
2.3936	1.6601282623079088	437	molecular function	10	cytoskeletal protein binding
2.3913	2.259431820927244	16757		401	molecular_function
2.3834	2.210925724557651	10046	cellular component	239	intracellular part
2.3831	2.2576280551010304	14761		352	cell part
2.3810	1.7727066993713378	243	biological process	6	regulation of kinase activity
2.3785	2.1435875109263827	4035	molecular function	96	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.