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	Value Type	Network Comparison Type	Rank	network_comparison	Interaction Map	green	red

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

description	Filtered	Value Type	Rank	network_comparison	Interaction Map	green	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	Measured	37	2.79409	High confidence	934.348	334.401
			131	1.31954	Low confidence	851.77	645.504
		Ranked	242	1.09822	High confidence	13895.8	15260.6
			629	1.02915	Low confidence	13590.3	13205.3
		Squared	37	10.2338	High confidence	1034.13	101.05
			146	1.63527	Low confidence	1268.51	775.72
		Rooted	53	1.5213	High confidence	18.0183	11.844
			537	1.04801	Low confidence	17.0804	16.298
	1	Measured	60	1.6231	High confidence	2765.82	4489.19
			4914	1.00597	Low confidence	7900.54	7853.62
		Ranked	18	1.32082	High confidence	245.247	185.678
			4130	1.01062	Low confidence	201.5	199.383
		Squared	245	1.31131	High confidence	6768.05	8875.01
			1119	1.04654	Low confidence	41688.5	43628.5
		Rooted	64	1.35128	High confidence	47.2654	63.8686
			4914	1.00944	Low confidence	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]		Measured	509	1.14278	High confidence	8630.06	7551.8
			885	1.03993	Low confidence	8585.64	8255.95
		Ranked	1038	1.03148	High confidence	181.041	186.741
			1328	1.02218	Low confidence	194.038	198.342
		Squared	295	1.27733	High confidence	39351.7	30807.7
			4562	1.01928	Low confidence	45736	46617.7
		Rooted	805	1.0645	High confidence	79.1513	74.3557
			1092	1.0386	Low confidence	76.3375	73.5001
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]		Measured	508	1.14293	High confidence	8636.87	7556.75
			880	1.04001	Low confidence	8587.03	8256.68
		Ranked	1032	1.03162	High confidence	180.943	186.664
			1322	1.0222	Low confidence	194.014	198.322
		Squared	294	1.2776	High confidence	39383.9	30826.5
			4569	1.01914	Low confidence	45740.5	46616.1
		Rooted	804	1.0646	High confidence	79.1931	74.3877
			1084	1.03863	Low confidence	76.3467	73.5068
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]		Measured	237	1.06457		9081.29	8530.51
			514	1.1411	High confidence	8532.02	7477
		Ranked	588	1.03039	Low confidence	185.859	191.507
			1048	1.031	High confidence	182.308	187.96
		Squared	311	1.27154		38866.5	30566.4
			4138	1.02676	Low confidence	47372.8	46138.2
		Rooted	378	1.04871		79.5804	75.8843
			822	1.06393	High confidence	78.5795	73.8577
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]		Measured	252	1.06194	Low confidence	9018.94	8492.92
			513	1.14143	High confidence	8543.66	7485.08
		Ranked	637	1.029	Low confidence	186.751	192.166
			1043	1.03128	High confidence	182.137	187.834
		Squared	308	1.27205		38919.9	30596.2
			4418	1.02256	Low confidence	47088.3	46049.4
		Rooted	427	1.04731		79.1997	75.6219
			811	1.06415	High confidence	78.6514	73.9102
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]		Measured	2035	1.03199	Low confidence	8323.04	8065.05
		Ranked	3423	1.01523		196.707	199.702

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.