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	green	red

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