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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.