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)	% Affected Genes	Class Size (#genes)	Class	Class	affected	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

Would Be Affected (#genes)	Average Regulation (ratio)	% Affected Genes	Class Size (#genes)	Class
21	2.5005394551489086	1.8711	1118	cellular developmental process
22	2.02202084991667	2.2167	974	ion transport
23	2.2058627247810363	2.0161	1164	negative regulation of cellular process
		1.8957	1238	negative regulation of biological process
	1.8484420895576477	4.3573	535	regulation of progression through cell cycle
		4.3197	539	regulation of cell cycle
25	1.9621534997766668	2.4123	1036	positive regulation of cellular process
26	2.644248050451279	2.1413	1204	organelle organization and biogenesis
	1.9786490954850848	1.8357	1417	biosynthetic process
27	1.8924930147502734	3.5604	746	cell cycle process
28	2.4829982866843543	3.0968	890	phosphate metabolic process
				phosphorus metabolic process
29	2.017735466957092	2.4655	1165	positive regulation of biological process
33	2.7678764888218472	2.6820	1217	intracellular signaling cascade
	2.1811264465595115	2.6103	1273	anatomical structure development
34	2.416864479581515	2.3483	1453	G-protein coupled receptor protein signaling pathway
37	2.403050871690114	3.0060	1226	response to stress
42	2.630213709672292	2.6362	1588	transcription
	2.43051519464044	2.0821	2008	cellular component organization and biogenesis
43	2.4479837675352356	2.9529	1442	post-translational protein modification
46	2.395317418234689	2.2307	2077	cell surface receptor linked signal transduction
48	1.9769652134332902	2.0945	2294	multicellular organismal process
52	2.470501118236118	3.0405	1721	protein modification process
		2.9393	1780	biopolymer modification
62	2.3732517415826972	2.5375	2448	regulation of transcription, DNA-dependent
66	2.3038527108075324	2.4081	2739	developmental process
67	2.4306948675828823	2.1879	3075	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
68	2.044925112809454	2.3304	2906	transport
69	2.3178554457061145	2.6245	2628	regulation of transcription
70	2.5307046931523542	2.3508	2985	response to stimulus
	2.2985232734680174	2.5907	2698	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	2.0665640378820487	2.3577	2969	establishment of localization
72	2.2670372059712043	2.4610	2913	regulation of cellular metabolic process
73	2.248631090488074	2.4047	3018	regulation of metabolic process
84	2.365392540051387	2.5312	3325	cellular protein metabolic process
		2.4857	3377	cellular macromolecule metabolic process
88	2.3753860882350377	2.3133	3816	signal transduction
89	2.408202938131384	2.6038	3425	biopolymer metabolic process
90	2.328269682611738	2.5307	3555	protein metabolic process
96	2.312502180275164	2.3114	4136	cell communication
104	2.1234114333987235	2.3959	4348	regulation of cellular process
110	2.089855896725374	2.3262	4730	regulation of biological process
120	2.0664001241807015	2.2856	5267	biological regulation
130	2.374769774137759	2.4068	5408	macromolecule metabolic process
178	2.357159194284982	2.4343	7318	primary metabolic process
181	2.3858967367693675	2.4996	7233	cellular metabolic process
208	2.3636351216514155	2.5270	8234	metabolic process
294	2.252760338363143	2.4522	11986	cellular process
377	2.246480769722174	2.4413	15431	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.