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)	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
2.420156256183163	2.5757	121	nucleus	4692	cellular component
2.416864479581515	2.3483	34	G-protein coupled receptor protein signaling pathway	1453	biological process
2.4153901100158692	2.0161	6	potassium ion transport	292
2.4113256633281708	4.7059	10	ice binding	216	molecular function
			response to freezing		biological process
			water binding		molecular function
	4.6784		homoiothermy	217	biological process
	4.4444		thermoregulation	226
2.410263843006558	2.0443	47	protein complex	2308	cellular component
2.4100664528933438	2.2358	13	protein-tyrosine kinase activity	565	molecular function
2.408202938131384	2.6038	89	biopolymer metabolic process	3425	biological process
2.403050871690114	3.0060	37	response to stress	1226
2.4005173126856487	2.0492	20	oxidoreductase activity	955	molecular function
2.3990859508514406	2.2422	6	soluble fraction	256	cellular component
2.3975469536251492	2.9801	10	positive regulation of transcription	338	biological process
	2.8939		positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	347
2.3974582254886627	3.4272	36	transcription factor activity	1038	molecular function
2.395317418234689	2.2307	46	cell surface receptor linked signal transduction	2077	biological process
2.3925783783197403	3.8095	9	enzyme linked receptor protein signaling pathway	230
2.3858967367693675	2.4996	181	cellular metabolic process	7233
2.383645436980508	2.1318	13	cellular lipid metabolic process	619
2.3829759624269276	2.1687	11	ion channel activity	494	molecular function
	2.0882		alpha-type channel activity	511
	2.0362		channel or pore class transporter activity	526
2.3798144817352296	3.2258	12	alcohol metabolic process	378	biological process
2.3753860882350377	2.3133	88	signal transduction	3816
2.374769774137759	2.4068	130	macromolecule metabolic process	5408
2.3732517415826972	2.5375	62	regulation of transcription, DNA-dependent	2448
2.3674656118665425	2.8226	45	transcription regulator activity	1596	molecular function
2.365392540051387	2.5312	84	cellular protein metabolic process	3325	biological process
	2.4857		cellular macromolecule metabolic process	3377
2.3636351216514155	2.5270	208	metabolic process	8234
2.3607054107329426	2.6235	20	protein transport	768
	2.4781		establishment of protein localization	810
2.357159194284982	2.4343	178	primary metabolic process	7318
2.35489083105518	1.7888	43	receptor activity	2420	molecular function
2.352012404373714	2.0339	57	macromolecular complex	2795	cellular component
2.3509053725462694	4.1270	17	GTP binding	417	molecular function
	4.0248		guanyl nucleotide binding	427
2.3492729663848877	1.8254	33	transmembrane receptor activity	1795
2.3445084154605866	1.8735	54	molecular transducer activity	2886
			signal transducer activity
2.3416898921132088	2.1592	25	structural molecule activity	1142
2.3321453965071477	2.2140	77	cytoplasm	3458	cellular component
2.331825590133667	2.0492	7	carbohydrate binding	333	molecular function
2.329086923599243	5.1546	6	embryonic morphogenesis	107	biological process
2.328269682611738	2.5307	90	protein metabolic process	3555
2.319896697998047	2.5057	13	intracellular protein transport	534
2.3178554457061145	2.6245	69	regulation of transcription	2628
2.317225064550127	1.7677	9	extracellular space	510	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.