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

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.