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