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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Gene	Filtered	description	Rank	Interaction Map	green	Value Type	red	network_comparison	Network Comparison Type

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

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