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	Would Be Affected (#genes)	Class Size (#genes)	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 75 to 124 of 173 in total

Class  : biological process

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

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.