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

Results: HTML CSV LaTeX

Showing element 125 to 174 of 328 in total

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class	Class
2.3127479553222656	6	1.4970	398	biological process	behavior
2.312502180275164	96	2.3114	4136		cell communication
2.3059755516052247	64	2.2085	2892	cellular component	intracellular organelle part
		2.2017	2900		organelle part
2.3038527108075324	66	2.4081	2739	biological process	developmental process
2.3028621958649675	65	2.4798	2641	molecular function	DNA binding
2.299432896077633	20	1.8561	1060	cellular component	integral to plasma membrane
		1.8286	1077		intrinsic to plasma membrane
2.2985232734680174	70	2.5907	2698	biological process	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.28793443441391	11	2.6247	429		positive regulation of cellular metabolic process
		2.4631	456		positive regulation of metabolic process
2.2792132452352725	96	2.5000	3858	molecular function	nucleic acid binding
2.2737072706222534	17	2.2364	752	biological process	lipid metabolic process
2.2681225514251913	179	2.4354	7366	molecular function	protein binding
2.267966568470001	7	3.9735	164	biological process	transmembrane receptor protein tyrosine kinase signaling pathway
2.2671763740532787	374	2.3725	15762	cellular component	cellular_component
2.2670372059712043	72	2.4610	2913	biological process	regulation of cellular metabolic process
2.2664323395275208	452	2.4356	18539	universal	all
2.266423319776853	28	2.9091	972	cellular component	cell fraction
2.2609615601026096	18	2.4030	734	molecular function	peptidase activity
2.2604436332529243	14	2.2267	634	biological process	response to external stimulus
2.2601398825645447	7	1.5228	464		monovalent inorganic cation transport
2.259431820927244	401	2.3913	16757	molecular function	molecular_function
2.2576280551010304	352	2.3831	14761	cellular component	cell part
2.2540424267450967	7	1.9608	358	biological process	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.252760338363143	294	2.4522	11986		cellular process
2.248631090488074	73	2.4047	3018		regulation of metabolic process
2.246480769722174	377	2.4413	15431		biological_process
2.243723976612091	15	2.0202	762		macromolecule biosynthetic process
2.241470267334763	319	2.4400	13082	molecular function	binding
2.2348088707242693	8	2.5271	321	biological process	nervous system development
2.2326475211552212		1.9608	414		negative regulation of cellular metabolic process
2.231512101073014	22	3.0400	739	cellular component	membrane fraction
2.2257004976272583	9	1.8248	497	molecular function	olfactory receptor activity
2.2204760638150303	14	1.6923	826	cellular component	extracellular region part
2.220401409599516	53	2.2099	2403	molecular function	zinc ion binding
2.216642654982189	192	2.4279	7902	cellular component	intracellular organelle
		2.4275	7904		organelle
2.2164768129587173	9	3.4335	264	biological process	organ morphogenesis
2.215940025315356	170	2.4157	7030	cellular component	intracellular membrane-bound organelle
					membrane-bound organelle
2.210925724557651	239	2.3834	10046		intracellular part
2.2093183655257618	137	2.3335	5858	molecular function	catalytic activity
2.2058627247810363	23	2.0161	1164	biological process	negative regulation of cellular process
		1.8957	1238		negative regulation of biological process
2.201751559972763		1.8244	1284	molecular function	G-protein coupled receptor activity
2.201178240776062	24	3.3727	723		hydrolase activity, acting on ester bonds
2.195966625213623	14	1.9569	696	cellular component	cytoskeletal part
2.1927802711725235	20	3.4188	579	molecular function	sequence-specific DNA binding
2.1918027877807615	12	2.0661	569	biological process	metal ion transport

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.