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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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