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	description	Filtered	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

Network Comparison Type  : Divided

description	Filtered	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]	0	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
	1	18	High confidence	245.247		185.678	1.32082
		60		2765.82	Measured	4489.19	1.6231
		64		47.2654	Rooted	63.8686	1.35128
		245		6768.05	Squared	8875.01	1.31131
		1119	Low confidence	41688.5		43628.5	1.04654
		4130		201.5	Ranked	199.383	1.01062
		4914		72.6287	Rooted	71.9496	1.00944
				7900.54	Measured	7853.62	1.00597
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]		295	High confidence	39351.7	Squared	30807.7	1.27733
		509		8630.06	Measured	7551.8	1.14278
		805		79.1513	Rooted	74.3557	1.0645
		885	Low confidence	8585.64	Measured	8255.95	1.03993
		1038	High confidence	181.041	Ranked	186.741	1.03148
		1092	Low confidence	76.3375	Rooted	73.5001	1.0386
		1328		194.038	Ranked	198.342	1.02218
		4562		45736	Squared	46617.7	1.01928
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]		294	High confidence	39383.9		30826.5	1.2776
		508		8636.87	Measured	7556.75	1.14293
		804		79.1931	Rooted	74.3877	1.0646
		880	Low confidence	8587.03	Measured	8256.68	1.04001
		1032	High confidence	180.943	Ranked	186.664	1.03162
		1084	Low confidence	76.3467	Rooted	73.5068	1.03863
		1322		194.014	Ranked	198.322	1.0222
		4569		45740.5	Squared	46616.1	1.01914
1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]		237		9081.29	Measured	8530.51	1.06457
		311	High confidence	38866.5	Squared	30566.4	1.27154
		378	Low confidence	79.5804	Rooted	75.8843	1.04871
		514	High confidence	8532.02	Measured	7477	1.1411
		588	Low confidence	185.859	Ranked	191.507	1.03039
		822	High confidence	78.5795	Rooted	73.8577	1.06393
		1048		182.308	Ranked	187.96	1.031
		4138	Low confidence	47372.8	Squared	46138.2	1.02676
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]		252		9018.94	Measured	8492.92	1.06194
		308	High confidence	38919.9	Squared	30596.2	1.27205
		427	Low confidence	79.1997	Rooted	75.6219	1.04731
		513	High confidence	8543.66	Measured	7485.08	1.14143
		637	Low confidence	186.751	Ranked	192.166	1.029
		811	High confidence	78.6514	Rooted	73.9102	1.06415
		1043		182.137	Ranked	187.834	1.03128
		4418	Low confidence	47088.3	Squared	46049.4	1.02256
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]		2035		8323.04	Measured	8065.05	1.03199
		2766		74.9741	Rooted	72.5914	1.03282

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.