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 75 to 124 of 173 in total

Class  : biological process

Average Regulation (ratio)	Would Be Affected (#genes)	% Affected Genes	Class Size (#genes)	Class
2.3178554457061145	69	2.6245	2628	regulation of transcription
2.3127479553222656	6	1.4970	398	behavior
2.312502180275164	96	2.3114	4136	cell communication
2.3038527108075324	66	2.4081	2739	developmental process
2.2985232734680174	70	2.5907	2698	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.28793443441391	11	2.6247	429	positive regulation of cellular metabolic process
		2.4631	456	positive regulation of metabolic process
2.2737072706222534	17	2.2364	752	lipid metabolic process
2.267966568470001	7	3.9735	164	transmembrane receptor protein tyrosine kinase signaling pathway
2.2670372059712043	72	2.4610	2913	regulation of cellular metabolic process
2.2604436332529243	14	2.2267	634	response to external stimulus
2.2601398825645447	7	1.5228	464	monovalent inorganic cation transport
2.2540424267450967		1.9608	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.252760338363143	294	2.4522	11986	cellular process
2.248631090488074	73	2.4047	3018	regulation of metabolic process
2.246480769722174	377	2.4413	15431	biological_process
2.243723976612091	15	2.0202	762	macromolecule biosynthetic process
2.2348088707242693	8	2.5271	321	nervous system development
2.2326475211552212		1.9608	414	negative regulation of cellular metabolic process
2.2164768129587173	9	3.4335	264	organ morphogenesis
2.2058627247810363	23	2.0161	1164	negative regulation of cellular process
		1.8957	1238	negative regulation of biological process
2.1918027877807615	12	2.0661	569	metal ion transport
2.1811264465595115	33	2.6103	1273	anatomical structure development
2.1725611826952766	20	2.2398	914	establishment of cellular localization
2.1655175536870956	9	6.3492	142	protein amino acid dephosphorylation
		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

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.