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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
2.259546995162964	1.3889	1	tRNA aminoacylation for protein translation	79	biological process
	1.3514		aminoacyl-tRNA ligase activity	82	molecular function
			ligase activity, forming aminoacyl-tRNA and related compounds
			ligase activity, forming carbon-oxygen bonds
2.259431820927244	2.3913	401	molecular_function	16757
2.259032130241394	2.3077	3	leukocyte activation	146	biological process
	2.0408	4	cell activation	174
2.2586302757263184	4.8780	5	calcium channel activity	93	molecular function
2.2576280551010304	2.3831	352	cell part	14761	cellular component
2.255178689956665	3.8462	2	negative regulation of protein kinase activity	58	biological process
	3.7736		negative regulation of transferase activity	59
	2.6667		negative regulation of enzyme activity	89
2.2540424267450967	1.9608	7	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	358
2.252760338363143	2.4522	294	cellular process	11986
2.252472698688507	1.7544	2	transcription corepressor activity	119	molecular function
2.248631090488074	2.4047	73	regulation of metabolic process	3018	biological process
2.246480769722174	2.4413	377	biological_process	15431
2.243723976612091	2.0202	15	macromolecule biosynthetic process	762
2.241470267334763	2.4400	319	binding	13082	molecular function
2.2348088707242693	2.5271	8	nervous system development	321	biological process
2.2326475211552212	1.9608		negative regulation of cellular metabolic process	414
2.231512101073014	3.0400	22	membrane fraction	739	cellular component
2.2310752868652344	11.1111	3	actomyosin structure organization and biogenesis	25	biological process
	1.0582	2	actin cytoskeleton organization and biogenesis	224
	0.9950		actin filament-based process	237
2.2257004976272583	1.8248	9	olfactory receptor activity	497	molecular function
2.2204760638150303	1.6923	14	extracellular region part	826	cellular component
2.220401409599516	2.2099	53	zinc ion binding	2403	molecular function
2.216642654982189	2.4279	192	intracellular organelle	7902	cellular component
	2.4275		organelle	7904
2.2164768129587173	3.4335	9	organ morphogenesis	264	biological process
2.215940025315356	2.4157	170	intracellular membrane-bound organelle	7030	cellular component
			membrane-bound organelle
2.210925724557651	2.3834	239	intracellular part	10046
2.2093183655257618	2.3335	137	catalytic activity	5858	molecular function
2.208425521850586	4.3478	1	glucose transport	27	biological process
	4.1667		hexose transport	28
			monosaccharide transport
	2.0408		protein amino acid autophosphorylation	50
	1.9608		protein autoprocessing	53
	1.8868		carbohydrate transport	62
2.2058627247810363	2.0161	23	negative regulation of cellular process	1164
	1.8957		negative regulation of biological process	1238
2.201751559972763	1.8244		G-protein coupled receptor activity	1284	molecular function
2.201178240776062	3.3727	24	hydrolase activity, acting on ester bonds	723
2.195966625213623	1.9569	14	cytoskeletal part	696	cellular component
2.1933199167251587	1.6000	2	tRNA metabolic process	142	biological process
2.1927802711725235	3.4188	20	sequence-specific DNA binding	579	molecular function
2.1918027877807615	2.0661	12	metal ion transport	569	biological process
2.189393002362478	2.1594	110	integral to membrane	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.