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

Results: HTML CSV LaTeX

Showing element 125 to 173 of 173 in total

Class  : biological process

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