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 125 to 174 of 328 in total

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