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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 173 in total

Class  : biological process

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