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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Filtered	Gene	description	Value Type	Rank	Network Comparison Type	Interaction Map	network_comparison	red	green

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

description	Value Type	Rank	Interaction Map	network_comparison	red	green
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	37	High confidence	2.79409	334.401	934.348
		131	Low confidence	1.31954	645.504	851.77
	Ranked	242	High confidence	1.09822	15260.6	13895.8
		629	Low confidence	1.02915	13205.3	13590.3
	Squared	37	High confidence	10.2338	101.05	1034.13
		146	Low confidence	1.63527	775.72	1268.51
	Rooted	53	High confidence	1.5213	11.844	18.0183
		537	Low confidence	1.04801	16.298	17.0804
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	Measured	778		1.00902	4825.89	4869.42
	Ranked	627		1.02953	10347.7	10050.9
	Squared	815		1.00447	40270.8	40451
	Rooted	768		1.0106	39.0982	39.5126
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Measured	19	High confidence	11.6763	305.45	26.1599
		171	Low confidence	1.22585	222.779	181.734
	Ranked	47	High confidence	1.42943	12941.7	18499.2
		384	Low confidence	1.08587	13533.1	14695.2
	Squared	26	High confidence	128.828	44.3683	0.344399
		697	Low confidence	1.03806	307.765	296.481
	Rooted	26	High confidence	3.62106	13.7805	3.80565
		131	Low confidence	1.20585	11.365	9.42485
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Measured	451	High confidence	1.01545	2683.61	2642.79
		771	Low confidence	1.01017	1593.68	1609.88
	Ranked	379	High confidence	1.03909	11228.4	10806
		825	Low confidence	1.00181	11832.8	11854.2
	Squared	316	High confidence	1.17196	8620.27	7355.46
		763	Low confidence	1.01738	6603.33	6490.54
	Rooted	370	High confidence	1.04188	30.7424	32.0298
		793	Low confidence	1.00582	23.11	23.2445
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Measured	474	High confidence	1.00763	2281.12	2263.85
		785	Low confidence	1.00797	2349.9	2331.31
	Ranked	495	High confidence	1.00195	11725.2	11748.1
		665	Low confidence	1.02285	11801.6	11538
	Squared	328	High confidence	1.14785	6747.71	5878.56
		591	Low confidence	1.07533	15800.9	14694
	Rooted	458	High confidence	1.01531	28.0847	28.5146
		728	Low confidence	1.01548	26.1642	26.5693
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	Measured	492	High confidence	1.00159	5038.33	5046.33
		822	Low confidence
	Ranked	299	High confidence	1.07178	12338.7	11512.3
		453	Low confidence
	Squared	493	High confidence	1	17901.1	17901.1
		836	Low confidence
	Rooted	438	High confidence	1.025	43.8864	44.9836
		662	Low confidence
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Measured	438	High confidence	1.0252	2925.57	2853.65
		581	Low confidence	1.04278	2015.65	1932.95
	Ranked	327	High confidence	1.05751	9897.29	10466.5
		501	Low confidence	1.0588	10721.7	11352.1
	Squared	477	High confidence	1.0074	18353.1	18218.3
		703	Low confidence	1.03494	10851.4	10485.1

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.