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

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.