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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 173 in total

Class  : biological process

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