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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
2.420156256183163	2.5757	121	4692	nucleus	cellular component
2.416864479581515	2.3483	34	1453	G-protein coupled receptor protein signaling pathway	biological process
2.4153901100158692	2.0161	6	292	potassium ion transport
2.4113256633281708	4.7059	10	216	ice binding	molecular function
				response to freezing	biological process
				water binding	molecular function
	4.6784		217	homoiothermy	biological process
	4.4444		226	thermoregulation
2.410263843006558	2.0443	47	2308	protein complex	cellular component
2.4100664528933438	2.2358	13	565	protein-tyrosine kinase activity	molecular function
2.408202938131384	2.6038	89	3425	biopolymer metabolic process	biological process
2.403050871690114	3.0060	37	1226	response to stress
2.4005173126856487	2.0492	20	955	oxidoreductase activity	molecular function
2.3990859508514406	2.2422	6	256	soluble fraction	cellular component
2.3975469536251492	2.9801	10	338	positive regulation of transcription	biological process
	2.8939		347	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.3974582254886627	3.4272	36	1038	transcription factor activity	molecular function
2.395317418234689	2.2307	46	2077	cell surface receptor linked signal transduction	biological process
2.3925783783197403	3.8095	9	230	enzyme linked receptor protein signaling pathway
2.3858967367693675	2.4996	181	7233	cellular metabolic process
2.383645436980508	2.1318	13	619	cellular lipid metabolic process
2.3829759624269276	2.1687	11	494	ion channel activity	molecular function
	2.0882		511	alpha-type channel activity
	2.0362		526	channel or pore class transporter activity
2.3798144817352296	3.2258	12	378	alcohol metabolic process	biological process
2.3753860882350377	2.3133	88	3816	signal transduction
2.374769774137759	2.4068	130	5408	macromolecule metabolic 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

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.