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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Average Regulation (ratio)	Class	Class Size (#genes)	% Affected Genes
6	3.0316067695617677	microtubule-based process	231	2.7174
	2.9956377029418944	chromatin modification	195	2.9412
	2.844642996788025	nucleocytoplasmic transport	206	2.9070
	2.7829527854919434	sensory perception of light stimulus	212	2.8090
		visual perception	211	2.8249
	2.745920252799988	carbohydrate metabolic process	544	1.1390
	2.4346015453338623	negative regulation of transcription	325	1.8051
	2.4153901100158692	potassium ion transport	292	2.0161
	2.329086923599243	embryonic morphogenesis	107	5.1546
	2.3127479553222656	behavior	398	1.4970
	1.9687834978103638	catabolic process	704	0.8741
		cellular catabolic process	559	1.0870
	1.9144784212112427	positive regulation of cell proliferation	272	2.0661
	1.8477724552154542	cell-cell adhesion	287	2.1930
	1.7971266508102417	lipid biosynthetic process	275	2.1368
	1.7727066993713378	regulation of kinase activity	243	2.3810
		regulation of protein kinase activity	236	2.4510
		regulation of transferase activity	247	2.3364
	1.7531960964202882	mRNA metabolic process	289	1.9841
		mRNA processing	242	2.3364
	1.6556044340133667	anion transport	229	2.6596
	1.575242853164673	amino acid metabolic process	314	1.8727
	1.4007941484451294	positive regulation of apoptosis	250	2.3585
		positive regulation of programmed cell death	252	2.3364
	1.368695902824402	chemical homeostasis	260	2.2321
	1.3052469968795777	regulation of cell differentiation	170	3.3333
		regulation of developmental process	276	2.0492
7	2.6894871592521667	muscle development	117	5.7692
	2.267966568470001	transmembrane receptor protein tyrosine kinase signaling pathway	164	3.9735
	2.2601398825645447	monovalent inorganic cation transport	464	1.5228
	2.2540424267450967	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	358	1.9608
	1.9949067831039429	protein complex assembly	335	2.0833
	1.683560033639272	regulation of catalytic activity	501	1.4634
	1.6523104111353557	response to DNA damage stimulus	337	2.0202
	1.632481078306834	mitosis	142	4.7244
	1.5113894144694011	amino acid and derivative metabolic process	388	1.8293
	1.3425244291623433	cell division	222	3.0303
8	2.6829177481787547	regulation of growth	192	3.9773
	2.2348088707242693	nervous system development	321	2.5271
	2.2326475211552212	negative regulation of cellular metabolic process	414	1.9608
	2.158773183822632	response to endogenous stimulus	428	1.8421
	1.8230999537876673	RNA splicing	208	3.7234
	1.6467143297195435	cell cycle phase	229	3.4146
	1.6290612050465174	regulation of a molecular function	527	1.6092
	1.5929162161690849	amine metabolic process	463	1.7949
		nitrogen compound metabolic process	484	1.7157
	1.4910563230514526	electron transport	514	1.5748
9	2.8815125972032547	apoptosis	379	2.4922
		programmed cell death	381	2.4845
	2.6086528982434953	inflammatory response	318	2.9289

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.