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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 8866 in total

Average Regulation (ratio)	Class	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class
2.259546995162964	threonine-tRNA ligase activity	33.3333	1	3	molecular function
	threonyl-tRNA aminoacylation				biological process
	tRNA aminoacylation	1.3889		79
	tRNA aminoacylation for protein translation
2.259431820927244	molecular_function	2.3913	401	16757	molecular function
2.259032130241394	cell activation	2.0408	4	174	biological process
	leukocyte activation	2.3077	3	146
2.2586302757263184	calcium channel activity	4.8780	5	93	molecular function
2.2576280551010304	cell part	2.3831	352	14761	cellular component
2.255178689956665	negative regulation of enzyme activity	2.6667	2	89	biological process
	negative regulation of protein kinase activity	3.8462		58
	negative regulation of transferase activity	3.7736		59
2.2540424267450967	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.9608	7	358
2.252760338363143	cellular process	2.4522	294	11986
2.252472698688507	transcription corepressor activity	1.7544	2	119	molecular function
2.248631090488074	regulation of metabolic process	2.4047	73	3018	biological process
2.246480769722174	biological_process	2.4413	377	15431
2.243723976612091	macromolecule biosynthetic process	2.0202	15	762
2.241470267334763	binding	2.4400	319	13082	molecular function
2.2348088707242693	nervous system development	2.5271	8	321	biological process
2.2326475211552212	negative regulation of cellular metabolic process	1.9608		414
2.231512101073014	membrane fraction	3.0400	22	739	cellular component
2.2310752868652344	actin cytoskeleton organization and biogenesis	1.0582	2	224	biological process
	actin filament-based process	0.9950		237
	actomyosin structure organization and biogenesis	11.1111	3	25
2.2257004976272583	olfactory receptor activity	1.8248	9	497	molecular function
2.2204760638150303	extracellular region part	1.6923	14	826	cellular component
2.220401409599516	zinc ion binding	2.2099	53	2403	molecular function
2.216642654982189	intracellular organelle	2.4279	192	7902	cellular component
	organelle	2.4275		7904
2.2164768129587173	organ morphogenesis	3.4335	9	264	biological process
2.215940025315356	intracellular membrane-bound organelle	2.4157	170	7030	cellular component
	membrane-bound organelle
2.210925724557651	intracellular part	2.3834	239	10046
2.2093183655257618	catalytic activity	2.3335	137	5858	molecular function
2.208425521850586	carbohydrate transport	1.8868	1	62	biological process
	glucose transport	4.3478		27
	hexose transport	4.1667		28
	monosaccharide transport
	protein amino acid autophosphorylation	2.0408		50
	protein autoprocessing	1.9608		53
2.2058627247810363	negative regulation of biological process	1.8957	23	1238
	negative regulation of cellular process	2.0161		1164
2.201751559972763	G-protein coupled receptor activity	1.8244		1284	molecular function
2.201178240776062	hydrolase activity, acting on ester bonds	3.3727	24	723
2.195966625213623	cytoskeletal part	1.9569	14	696	cellular component
2.1933199167251587	tRNA metabolic process	1.6000	2	142	biological process
2.1927802711725235	sequence-specific DNA binding	3.4188	20	579	molecular function
2.1918027877807615	metal ion transport	2.0661	12	569	biological process
2.189393002362478	integral to membrane	2.1594	110	5089	cellular component

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.