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

Results: HTML CSV LaTeX

Showing element 175 to 224 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class	Class Size (#genes)	Class
3.284923235575358	1.2876	3	membrane organization and biogenesis	252	biological process
3.2791879177093506	12.5000	1	response to pain	8
	11.1111		calcium-dependent protein binding	11	molecular function
	9.0909		sensory perception of pain		biological process
	6.2500		specific transcriptional repressor activity	18	molecular function
3.243556241194407	5.4545	6	potassium ion binding	118
	3.4682	7	alkali metal ion binding	191
3.2296558618545532	3.2609	4	protein heterodimerization activity	119
3.2158093452453613	50.0000	1	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	2
			ATP-dependent polynucleotide kinase activity
			polydeoxyribonucleotide kinase activity
			polynucleotide kinase activity
	1.9608		nucleobase, nucleoside, nucleotide kinase activity	67
3.2147316932678223	20.0000		eukaryotic translation elongation factor 1 complex	7	cellular component
3.1892552375793457	1.3072	2	fatty acid metabolic process	172	biological process
3.175950493131365	2.5000	10	establishment and/or maintenance of chromatin architecture	416
	2.4561		DNA packaging	422
	2.0349		chromosome organization and biogenesis (sensu Eukaryota)	496
3.1701605319976807	13.3333	2	nuclear organization and biogenesis	17
3.1123706102371216	1.6260	3	response to other organism	209
3.102418303489685	1.3245		sugar binding	220	molecular function
3.0782742261886598	2.2026	15	defense response	680	biological process
3.075394868850708	6.2500	2	nuclear chromosome	36	cellular component
3.0503673553466797	20.0000	1	substrate-bound cell migration, cell extension	5	biological process
	1.8519		cell projection biogenesis	60
	1.1765		cell projection organization and biogenesis	94
	0.9259		cell morphogenesis	120
3.0427030324935913	3.9216	2	sodium:dicarboxylate symporter activity	62	molecular function
	3.7736		dicarboxylic acid transport	64	biological process
	3.7037		dicarboxylic acid transporter activity	65	molecular function
	2.9851		anion:cation symporter activity	80
	2.8169		organic acid:sodium symporter activity	83
3.0342323780059814	4.0000	1	kinetochore	25	cellular component
3.0316067695617677	2.7174	6	microtubule-based process	231	biological process
2.9956377029418944	2.9412		chromatin modification	195
2.9851186752319334	1.3369		lipid binding	448	molecular function
2.976668506860733	1.9900	5	cofactor binding	243
2.967112342516581	2.4194	4	cytosolic part	159	cellular component
2.9601402282714844	4.8000	9	chromatin	184
2.9439388116200766	1.5385	4	negative regulation of apoptosis	237	biological process
	1.5152		negative regulation of programmed cell death	240
2.941256210207939	2.1858	11	chromosome organization and biogenesis	519
2.938953399658203	6.2500	1	I-kappaB kinase/NF-kappaB cascade	20
2.9320233133104114	1.9459	21	transferase activity, transferring phosphorus-containing groups	1086	molecular function
2.927939693133036	3.0000	4	transmembrane receptor protein tyrosine kinase activity	125
	2.6549		transmembrane receptor protein kinase activity	140
2.9275668263435364	1.9417	2	skeletal development	119	biological process
2.9041290283203125	1.3423		endocytosis	162
	1.2903		membrane invagination	168
2.889312744140625	6.6667		condensed chromosome	35	cellular component

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.