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	Rank	green	network_comparison	Interaction Map	Value Type	red	Network Comparison Type

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

description	Rank	green	network_comparison	Interaction Map	Value Type	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	37	934.348	2.79409	High confidence	Measured	334.401
		1034.13	10.2338		Squared	101.05
	53	18.0183	1.5213		Rooted	11.844
	131	851.77	1.31954	Low confidence	Measured	645.504
	146	1268.51	1.63527		Squared	775.72
	242	13895.8	1.09822	High confidence	Ranked	15260.6
	537	17.0804	1.04801	Low confidence	Rooted	16.298
	629	13590.3	1.02915		Ranked	13205.3
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	627	10050.9	1.02953			10347.7
	768	39.5126	1.0106		Rooted	39.0982
	778	4869.42	1.00902		Measured	4825.89
	815	40451	1.00447		Squared	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]	19	26.1599	11.6763	High confidence	Measured	305.45
	26	0.344399	128.828		Squared	44.3683
		3.80565	3.62106		Rooted	13.7805
	47	18499.2	1.42943		Ranked	12941.7
	131	9.42485	1.20585	Low confidence	Rooted	11.365
	171	181.734	1.22585		Measured	222.779
	384	14695.2	1.08587		Ranked	13533.1
	697	296.481	1.03806		Squared	307.765
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	316	7355.46	1.17196	High confidence		8620.27
	370	32.0298	1.04188		Rooted	30.7424
	379	10806	1.03909		Ranked	11228.4
	451	2642.79	1.01545		Measured	2683.61
	763	6490.54	1.01738	Low confidence	Squared	6603.33
	771	1609.88	1.01017		Measured	1593.68
	793	23.2445	1.00582		Rooted	23.11
	825	11854.2	1.00181		Ranked	11832.8
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	328	5878.56	1.14785	High confidence	Squared	6747.71
	458	28.5146	1.01531		Rooted	28.0847
	474	2263.85	1.00763		Measured	2281.12
	495	11748.1	1.00195		Ranked	11725.2
	591	14694	1.07533	Low confidence	Squared	15800.9
	665	11538	1.02285		Ranked	11801.6
	728	26.5693	1.01548		Rooted	26.1642
	785	2331.31	1.00797		Measured	2349.9
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	299	11512.3	1.07178	High confidence	Ranked	12338.7
	438	44.9836	1.025		Rooted	43.8864
	453	11512.3	1.07178	Low confidence	Ranked	12338.7
	492	5046.33	1.00159	High confidence	Measured	5038.33
	493	17901.1	1		Squared	17901.1
	662	44.9836	1.025	Low confidence	Rooted	43.8864
	822	5046.33	1.00159		Measured	5038.33
	836	17901.1	1		Squared	17901.1
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	327	10466.5	1.05751	High confidence	Ranked	9897.29
	376	31.1453	1.03923		Rooted	32.3671
	438	2853.65	1.0252		Measured	2925.57
	442	25.4539	1.06963	Low confidence	Rooted	27.2263
	477	18218.3	1.0074	High confidence	Squared	18353.1
	501	11352.1	1.0588	Low confidence	Ranked	10721.7

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.