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	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

description	Rank	Value Type	Interaction Map	red	green	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	37	Measured	High confidence	334.401	934.348	2.79409
		Squared		101.05	1034.13	10.2338
	53	Rooted		11.844	18.0183	1.5213
	131	Measured	Low confidence	645.504	851.77	1.31954
	146	Squared		775.72	1268.51	1.63527
	242	Ranked	High confidence	15260.6	13895.8	1.09822
	537	Rooted	Low confidence	16.298	17.0804	1.04801
	629	Ranked		13205.3	13590.3	1.02915
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	627			10347.7	10050.9	1.02953
	768	Rooted		39.0982	39.5126	1.0106
	778	Measured		4825.89	4869.42	1.00902
	815	Squared		40270.8	40451	1.00447
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	Measured	High confidence	305.45	26.1599	11.6763
	26	Squared		44.3683	0.344399	128.828
		Rooted		13.7805	3.80565	3.62106
	47	Ranked		12941.7	18499.2	1.42943
	131	Rooted	Low confidence	11.365	9.42485	1.20585
	171	Measured		222.779	181.734	1.22585
	384	Ranked		13533.1	14695.2	1.08587
	697	Squared		307.765	296.481	1.03806
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	316		High confidence	8620.27	7355.46	1.17196
	370	Rooted		30.7424	32.0298	1.04188
	379	Ranked		11228.4	10806	1.03909
	451	Measured		2683.61	2642.79	1.01545
	763	Squared	Low confidence	6603.33	6490.54	1.01738
	771	Measured		1593.68	1609.88	1.01017
	793	Rooted		23.11	23.2445	1.00582
	825	Ranked		11832.8	11854.2	1.00181
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	328	Squared	High confidence	6747.71	5878.56	1.14785
	458	Rooted		28.0847	28.5146	1.01531
	474	Measured		2281.12	2263.85	1.00763
	495	Ranked		11725.2	11748.1	1.00195
	591	Squared	Low confidence	15800.9	14694	1.07533
	665	Ranked		11801.6	11538	1.02285
	728	Rooted		26.1642	26.5693	1.01548
	785	Measured		2349.9	2331.31	1.00797
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	299	Ranked	High confidence	12338.7	11512.3	1.07178
	438	Rooted		43.8864	44.9836	1.025
	453	Ranked	Low confidence	12338.7	11512.3	1.07178
	492	Measured	High confidence	5038.33	5046.33	1.00159
	493	Squared		17901.1	17901.1	1
	662	Rooted	Low confidence	43.8864	44.9836	1.025
	822	Measured		5038.33	5046.33	1.00159
	836	Squared		17901.1	17901.1	1
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	327	Ranked	High confidence	9897.29	10466.5	1.05751
	376	Rooted		32.3671	31.1453	1.03923
	438	Measured		2925.57	2853.65	1.0252
	442	Rooted	Low confidence	27.2263	25.4539	1.06963
	477	Squared	High confidence	18353.1	18218.3	1.0074
	501	Ranked	Low confidence	10721.7	11352.1	1.0588

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.