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	Microarray Measured (#genes)	affected	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 328 in total

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

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.