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

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.