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 Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 101 to 150 of 328 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
2.374769774137759	2.4068	130	5408	macromolecule metabolic process	biological process
2.3732517415826972	2.5375	62	2448	regulation of transcription, DNA-dependent
2.3674656118665425	2.8226	45	1596	transcription regulator activity	molecular function
2.365392540051387	2.5312	84	3325	cellular protein metabolic process	biological process
	2.4857		3377	cellular macromolecule metabolic process
2.3636351216514155	2.5270	208	8234	metabolic process
2.3607054107329426	2.6235	20	768	protein transport
	2.4781		810	establishment of protein localization
2.357159194284982	2.4343	178	7318	primary metabolic process
2.35489083105518	1.7888	43	2420	receptor activity	molecular function
2.352012404373714	2.0339	57	2795	macromolecular complex	cellular component
2.3509053725462694	4.1270	17	417	GTP binding	molecular function
	4.0248		427	guanyl nucleotide binding
2.3492729663848877	1.8254	33	1795	transmembrane receptor activity
2.3445084154605866	1.8735	54	2886	molecular transducer activity
				signal transducer activity
2.3416898921132088	2.1592	25	1142	structural molecule activity
2.3321453965071477	2.2140	77	3458	cytoplasm	cellular component
2.331825590133667	2.0492	7	333	carbohydrate binding	molecular function
2.329086923599243	5.1546	6	107	embryonic morphogenesis	biological process
2.328269682611738	2.5307	90	3555	protein metabolic process
2.319896697998047	2.5057	13	534	intracellular protein transport
2.3178554457061145	2.6245	69	2628	regulation of transcription
2.317225064550127	1.7677	9	510	extracellular space	cellular component
2.3127479553222656	1.4970	6	398	behavior	biological process
2.312502180275164	2.3114	96	4136	cell communication
2.3059755516052247	2.2085	64	2892	intracellular organelle part	cellular component
	2.2017		2900	organelle part
2.3038527108075324	2.4081	66	2739	developmental process	biological process
2.3028621958649675	2.4798	65	2641	DNA binding	molecular function
2.299432896077633	1.8561	20	1060	integral to plasma membrane	cellular component
	1.8286		1077	intrinsic to plasma membrane
2.2985232734680174	2.5907	70	2698	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	biological process
2.28793443441391	2.6247	11	429	positive regulation of cellular metabolic process
	2.4631		456	positive regulation of metabolic process
2.2792132452352725	2.5000	96	3858	nucleic acid binding	molecular function
2.2737072706222534	2.2364	17	752	lipid metabolic process	biological process
2.2681225514251913	2.4354	179	7366	protein binding	molecular function
2.267966568470001	3.9735	7	164	transmembrane receptor protein tyrosine kinase signaling pathway	biological process
2.2671763740532787	2.3725	374	15762	cellular_component	cellular component
2.2670372059712043	2.4610	72	2913	regulation of cellular metabolic process	biological process
2.2664323395275208	2.4356	452	18539	all	universal
2.266423319776853	2.9091	28	972	cell fraction	cellular component
2.2609615601026096	2.4030	18	734	peptidase activity	molecular function
2.2604436332529243	2.2267	14	634	response to external stimulus	biological process
2.2601398825645447	1.5228	7	464	monovalent inorganic cation transport
2.259431820927244	2.3913	401	16757	molecular_function	molecular function
2.2576280551010304	2.3831	352	14761	cell part	cellular component
2.2540424267450967	1.9608	7	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	biological process
2.252760338363143	2.4522	294	11986	cellular process

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.