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 Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 173 in total

Class  : biological process

% Affected Genes	Would Be Affected (#genes)	Average Regulation (ratio)	Class Size (#genes)	Class
2.4610	72	2.2670372059712043	2913	regulation of cellular metabolic process
2.4561	10	3.175950493131365	422	DNA packaging
2.4522	294	2.252760338363143	11986	cellular process
2.4510	6	1.7727066993713378	236	regulation of protein kinase activity
2.4413	377	2.246480769722174	15431	biological_process
2.4343	178	2.357159194284982	7318	primary metabolic process
2.4272	11	2.0707096576690676	466	system development
2.4123	25	1.9621534997766668	1036	positive regulation of cellular process
2.4081	66	2.3038527108075324	2739	developmental process
2.4068	130	2.374769774137759	5408	macromolecule metabolic process
2.4064	11	2.6960288683573403	442	small GTPase mediated signal transduction
2.4047	73	2.248631090488074	3018	regulation of metabolic process
2.3959	104	2.1234114333987235	4348	regulation of cellular process
2.3810	6	1.7727066993713378	243	regulation of kinase activity
2.3679	16	2.0103142169805674	660	regulation of biological quality
2.3585	6	1.4007941484451294	250	positive regulation of apoptosis
2.3577	70	2.0665640378820487	2969	establishment of localization
2.3508		2.5307046931523542	2985	response to stimulus
2.3483	34	2.416864479581515	1453	G-protein coupled receptor protein signaling pathway
2.3364	6	1.7727066993713378	247	regulation of transferase activity
		1.7531960964202882	242	mRNA processing
		1.4007941484451294	252	positive regulation of programmed cell death
2.3304	68	2.044925112809454	2906	transport
2.3262	110	2.089855896725374	4730	regulation of biological process
2.3133	88	2.3753860882350377	3816	signal transduction
2.3114	96	2.312502180275164	4136	cell communication
2.2856	120	2.0664001241807015	5267	biological regulation
2.2670	10	1.8413102626800537	448	RNA processing
2.2514	16	2.4382004340489707	732	sensory perception
2.2398	20	2.1725611826952766	914	establishment of cellular localization
2.2364	17	2.2737072706222534	752	lipid metabolic process
2.2321	6	1.368695902824402	260	chemical homeostasis
2.2307	46	2.395317418234689	2077	cell surface receptor linked signal transduction
2.2267	14	2.2604436332529243	634	response to external stimulus
2.2184	20	2.6115847550905666	879	immune system process
2.2181	16	2.4382004340489707	741	neurological process
2.2167	22	2.02202084991667	974	ion transport
2.2026	15	3.0782742261886598	680	defense response
2.1930	6	1.8477724552154542	287	cell-cell adhesion
2.1879	67	2.4306948675828823	3075	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.1858	11	2.941256210207939	519	chromosome organization and biogenesis
2.1417	17	1.9759902954101562	800	proteolysis
2.1413	26	2.644248050451279	1204	organelle organization and biogenesis
2.1407	17	1.8383450422968184	806	biological adhesion
				cell adhesion
2.1390	9	2.1474349200725555	432	cell motility
2.1368	6	1.7971266508102417	275	lipid biosynthetic process
2.1318	13	2.383645436980508	619	cellular lipid metabolic process
2.1164	14	2.105520764986674	669	cation transport
2.0992	13	2.114047809080644	633	response to chemical stimulus

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.