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 [...,...].

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 101 to 150 of 173 in total

Class  : biological process

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class
2.1655175536870956	9	5.7143	158	dephosphorylation
2.16537378515516	17	2.0202	840	intracellular transport
2.158773183822632	8	1.8421	428	response to endogenous stimulus
2.1474349200725555	9	2.1390	432	cell motility
2.1418599311043236	19	2.8333	686	anatomical structure morphogenesis
2.123886121643914	11	2.0179	534	regulation of apoptosis
		1.9912	540	regulation of programmed cell death
2.1234114333987235	104	2.3959	4348	regulation of cellular process
2.121824940045675	10	1.9824	510	vesicle-mediated transport
2.1211151123046874	13	2.0325	663	macromolecular complex assembly
		1.9120	701	cellular component assembly
2.1150057166814804	9	2.0202	460	negative regulation of metabolic process
2.114047809080644	13	2.0992	633	response to chemical stimulus
2.105520764986674	14	2.1164	669	cation transport
2.0980815972600664	16	1.9204	832	RNA metabolic process
2.089855896725374	110	2.3262	4730	regulation of biological process
2.0859246611595155	11	1.5773	727	cell differentiation
2.0707096576690676		2.4272	466	system development
2.0665640378820487	70	2.3577	2969	establishment of localization
2.0664001241807015	120	2.2856	5267	biological regulation
2.046714186668396	9	2.5078	370	cell proliferation
2.044925112809454	68	2.3304	2906	transport
2.02202084991667	22	2.2167	974	ion transport
2.017735466957092	29	2.4655	1165	positive regulation of biological process
2.0103142169805674	16	2.5048	623	homeostatic process
		2.3679	660	regulation of biological quality
1.9949067831039429	7	2.0833	335	protein complex assembly
1.9786490954850848	26	1.8357	1417	biosynthetic process
1.9769652134332902	48	2.0945	2294	multicellular organismal process
1.9759902954101562	17	2.1417	800	proteolysis
1.9687834978103638	6	1.0870	559	cellular catabolic process
		0.8741	704	catabolic process
1.9621534997766668	25	2.4123	1036	positive regulation of cellular process
1.9346576482057571	11	1.6701	629	generation of precursor metabolites and energy
1.9312101155519485	9	1.6327	570	carboxylic acid metabolic process
		1.6227	573	organic acid metabolic process
1.9144784212112427	6	2.0661	272	positive regulation of cell proliferation
1.8924930147502734	27	3.5604	746	cell cycle process
1.8484420895576477	23	4.3573	535	regulation of progression through cell cycle
		4.3197	539	regulation of cell cycle
1.8477724552154542	6	2.1930	287	cell-cell adhesion
1.8413102626800537	10	2.2670	448	RNA processing
1.8383450422968184	17	2.1407	806	biological adhesion
				cell adhesion
1.8230999537876673	8	3.7234	208	RNA splicing
1.7971266508102417	6	2.1368	275	lipid biosynthetic process
1.7727066993713378		2.4510	236	regulation of protein kinase activity
		2.3810	243	regulation of kinase activity
		2.3364	247	regulation of transferase activity
1.7531960964202882			242	mRNA processing

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.