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