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