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

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Showing element 1 to 50 of 38536 in total

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Network Comparison Type  : Divided

description	green	Value Type	Interaction Map	network_comparison	Rank	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	17.0804	Rooted	Low confidence	1.04801	537	16.298
	18.0183		High confidence	1.5213	53	11.844
	851.77	Measured	Low confidence	1.31954	131	645.504
	934.348		High confidence	2.79409	37	334.401
	1034.13	Squared		10.2338		101.05
	1268.51		Low confidence	1.63527	146	775.72
	13590.3	Ranked		1.02915	629	13205.3
	13895.8		High confidence	1.09822	242	15260.6
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	39.5126	Rooted	Low confidence	1.0106	768	39.0982
	4869.42	Measured		1.00902	778	4825.89
	10050.9	Ranked		1.02953	627	10347.7
	40451	Squared		1.00447	815	40270.8
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]	0.344399		High confidence	128.828	26	44.3683
	3.80565	Rooted		3.62106		13.7805
	9.42485		Low confidence	1.20585	131	11.365
	26.1599	Measured	High confidence	11.6763	19	305.45
	181.734		Low confidence	1.22585	171	222.779
	296.481	Squared		1.03806	697	307.765
	14695.2	Ranked		1.08587	384	13533.1
	18499.2		High confidence	1.42943	47	12941.7
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	23.2445	Rooted	Low confidence	1.00582	793	23.11
	32.0298		High confidence	1.04188	370	30.7424
	1609.88	Measured	Low confidence	1.01017	771	1593.68
	2642.79		High confidence	1.01545	451	2683.61
	6490.54	Squared	Low confidence	1.01738	763	6603.33
	7355.46		High confidence	1.17196	316	8620.27
	10806	Ranked		1.03909	379	11228.4
	11854.2		Low confidence	1.00181	825	11832.8
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	26.5693	Rooted		1.01548	728	26.1642
	28.5146		High confidence	1.01531	458	28.0847
	2263.85	Measured		1.00763	474	2281.12
	2331.31		Low confidence	1.00797	785	2349.9
	5878.56	Squared	High confidence	1.14785	328	6747.71
	11538	Ranked	Low confidence	1.02285	665	11801.6
	11748.1		High confidence	1.00195	495	11725.2
	14694	Squared	Low confidence	1.07533	591	15800.9
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	44.9836	Rooted	High confidence	1.025	438	43.8864
			Low confidence		662
	5046.33	Measured	High confidence	1.00159	492	5038.33
			Low confidence		822
	11512.3	Ranked	High confidence	1.07178	299	12338.7
			Low confidence		453
	17901.1	Squared	High confidence	1	493	17901.1
			Low confidence		836
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	25.4539	Rooted		1.06963	442	27.2263
	31.1453		High confidence	1.03923	376	32.3671
	1932.95	Measured	Low confidence	1.04278	581	2015.65
	2853.65		High confidence	1.0252	438	2925.57
	10466.5	Ranked		1.05751	327	9897.29
	10485.1	Squared	Low confidence	1.03494	703	10851.4

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.