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