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	Network Comparison Type	Rank	Interaction Map	Value Type	network_comparison	green	red

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

description	Filtered	Rank	Interaction Map	Value Type	network_comparison	green	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	37	High confidence	Measured	2.79409	934.348	334.401
				Squared	10.2338	1034.13	101.05
		53		Rooted	1.5213	18.0183	11.844
		131	Low confidence	Measured	1.31954	851.77	645.504
		146		Squared	1.63527	1268.51	775.72
		242	High confidence	Ranked	1.09822	13895.8	15260.6
		537	Low confidence	Rooted	1.04801	17.0804	16.298
		629		Ranked	1.02915	13590.3	13205.3
	1	18	High confidence		1.32082	245.247	185.678
		60		Measured	1.6231	2765.82	4489.19
		64		Rooted	1.35128	47.2654	63.8686
		245		Squared	1.31131	6768.05	8875.01
		1119	Low confidence		1.04654	41688.5	43628.5
		4130		Ranked	1.01062	201.5	199.383
		4914		Measured	1.00597	7900.54	7853.62
				Rooted	1.00944	72.6287	71.9496
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	Squared	1.27733	39351.7	30807.7
		509		Measured	1.14278	8630.06	7551.8
		805		Rooted	1.0645	79.1513	74.3557
		885	Low confidence	Measured	1.03993	8585.64	8255.95
		1038	High confidence	Ranked	1.03148	181.041	186.741
		1092	Low confidence	Rooted	1.0386	76.3375	73.5001
		1328		Ranked	1.02218	194.038	198.342
		4562		Squared	1.01928	45736	46617.7
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		1.2776	39383.9	30826.5
		508		Measured	1.14293	8636.87	7556.75
		804		Rooted	1.0646	79.1931	74.3877
		880	Low confidence	Measured	1.04001	8587.03	8256.68
		1032	High confidence	Ranked	1.03162	180.943	186.664
		1084	Low confidence	Rooted	1.03863	76.3467	73.5068
		1322		Ranked	1.0222	194.014	198.322
		4569		Squared	1.01914	45740.5	46616.1
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		Measured	1.06457	9081.29	8530.51
		311	High confidence	Squared	1.27154	38866.5	30566.4
		378	Low confidence	Rooted	1.04871	79.5804	75.8843
		514	High confidence	Measured	1.1411	8532.02	7477
		588	Low confidence	Ranked	1.03039	185.859	191.507
		822	High confidence	Rooted	1.06393	78.5795	73.8577
		1048		Ranked	1.031	182.308	187.96
		4138	Low confidence	Squared	1.02676	47372.8	46138.2
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		Measured	1.06194	9018.94	8492.92
		308	High confidence	Squared	1.27205	38919.9	30596.2
		427	Low confidence	Rooted	1.04731	79.1997	75.6219
		513	High confidence	Measured	1.14143	8543.66	7485.08
		637	Low confidence	Ranked	1.029	186.751	192.166
		811	High confidence	Rooted	1.06415	78.6514	73.9102
		1043		Ranked	1.03128	182.137	187.834
		4418	Low confidence	Squared	1.02256	47088.3	46049.4
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]		2035		Measured	1.03199	8323.04	8065.05
		2766		Rooted	1.03282	74.9741	72.5914

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.