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