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 [...,...].

% Affected Genes	Average Regulation (ratio)	Class	Would Be Affected (#genes)	Class Size (#genes)	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 173 in total

Class  : biological process

% Affected Genes	Average Regulation (ratio)	Class	Would Be Affected (#genes)	Class Size (#genes)
2.6038	2.408202938131384	biopolymer metabolic process	89	3425
2.5907	2.2985232734680174	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	70	2698
2.5890	2.6417386531829834	phosphorylation	18	711
2.5554	2.5815784772237143	protein amino acid phosphorylation	17	675
2.5375	2.3732517415826972	regulation of transcription, DNA-dependent	62	2448
2.5312	2.365392540051387	cellular protein metabolic process	84	3325
2.5307	2.328269682611738	protein metabolic process	90	3555
2.5271	2.2348088707242693	nervous system development	8	321
2.5270	2.3636351216514155	metabolic process	208	8234
2.5172	1.6883443919095127	cell-cell signaling	13	514
2.5078	2.046714186668396	cell proliferation	9	370
2.5057	2.319896697998047	intracellular protein transport	13	534
2.5048	2.0103142169805674	homeostatic process	16	623
2.5045	2.539123611790793	organ development		644
2.5000	3.175950493131365	establishment and/or maintenance of chromatin architecture	10	416
2.4996	2.3858967367693675	cellular metabolic process	181	7233
2.4922	2.8815125972032547	apoptosis	9	379
2.4857	2.365392540051387	cellular macromolecule metabolic process	84	3377
2.4845	2.8815125972032547	programmed cell death	9	381
2.4781	2.3607054107329426	establishment of protein localization	20	810
2.4658	2.8162122435039945	cell death	11	430
		death
2.4655	2.017735466957092	positive regulation of biological process	29	1165
2.4631	2.28793443441391	positive regulation of metabolic process	11	456
2.4610	2.2670372059712043	regulation of cellular metabolic process	72	2913
2.4561	3.175950493131365	DNA packaging	10	422
2.4522	2.252760338363143	cellular process	294	11986
2.4510	1.7727066993713378	regulation of protein kinase activity	6	236
2.4413	2.246480769722174	biological_process	377	15431
2.4343	2.357159194284982	primary metabolic process	178	7318
2.4272	2.0707096576690676	system development	11	466
2.4123	1.9621534997766668	positive regulation of cellular process	25	1036
2.4081	2.3038527108075324	developmental process	66	2739
2.4068	2.374769774137759	macromolecule metabolic process	130	5408
2.4064	2.6960288683573403	small GTPase mediated signal transduction	11	442
2.4047	2.248631090488074	regulation of metabolic process	73	3018
2.3959	2.1234114333987235	regulation of cellular process	104	4348
2.3810	1.7727066993713378	regulation of kinase activity	6	243
2.3679	2.0103142169805674	regulation of biological quality	16	660
2.3585	1.4007941484451294	positive regulation of apoptosis	6	250
2.3577	2.0665640378820487	establishment of localization	70	2969
2.3508	2.5307046931523542	response to stimulus		2985
2.3483	2.416864479581515	G-protein coupled receptor protein signaling pathway	34	1453
2.3364	1.7727066993713378	regulation of transferase activity	6	247
	1.7531960964202882	mRNA processing		242
	1.4007941484451294	positive regulation of programmed cell death		252
2.3304	2.044925112809454	transport	68	2906
2.3262	2.089855896725374	regulation of biological process	110	4730
2.3133	2.3753860882350377	signal transduction	88	3816
2.3114	2.312502180275164	cell communication	96	4136

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.