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

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Showing element 1 to 50 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	Value Type	Interaction Map	green	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	Ranked	High confidence	245.247	185.678	1.32082
	60	Measured		2765.82	4489.19	1.6231
	64	Rooted		47.2654	63.8686	1.35128
	245	Squared		6768.05	8875.01	1.31131
	1119		Low confidence	41688.5	43628.5	1.04654
	4130	Ranked		201.5	199.383	1.01062
	4914	Measured		7900.54	7853.62	1.00597
		Rooted		72.6287	71.9496	1.00944
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	High confidence	39351.7	30807.7	1.27733
	509	Measured		8630.06	7551.8	1.14278
	805	Rooted		79.1513	74.3557	1.0645
	885	Measured	Low confidence	8585.64	8255.95	1.03993
	1038	Ranked	High confidence	181.041	186.741	1.03148
	1092	Rooted	Low confidence	76.3375	73.5001	1.0386
	1328	Ranked		194.038	198.342	1.02218
	4562	Squared		45736	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	Measured		8636.87	7556.75	1.14293
	804	Rooted		79.1931	74.3877	1.0646
	880	Measured	Low confidence	8587.03	8256.68	1.04001
	1032	Ranked	High confidence	180.943	186.664	1.03162
	1084	Rooted	Low confidence	76.3467	73.5068	1.03863
	1322	Ranked		194.014	198.322	1.0222
	4569	Squared		45740.5	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	Measured		9081.29	8530.51	1.06457
	311	Squared	High confidence	38866.5	30566.4	1.27154
	378	Rooted	Low confidence	79.5804	75.8843	1.04871
	514	Measured	High confidence	8532.02	7477	1.1411
	588	Ranked	Low confidence	185.859	191.507	1.03039
	822	Rooted	High confidence	78.5795	73.8577	1.06393
	1048	Ranked		182.308	187.96	1.031
	4138	Squared	Low confidence	47372.8	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	Measured		9018.94	8492.92	1.06194
	308	Squared	High confidence	38919.9	30596.2	1.27205
	427	Rooted	Low confidence	79.1997	75.6219	1.04731
	513	Measured	High confidence	8543.66	7485.08	1.14143
	637	Ranked	Low confidence	186.751	192.166	1.029
	811	Rooted	High confidence	78.6514	73.9102	1.06415
	1043	Ranked		182.137	187.834	1.03128
	4418	Squared	Low confidence	47088.3	46049.4	1.02256
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	2035	Measured		8323.04	8065.05	1.03199
	2766	Rooted		74.9741	72.5914	1.03282
	3423	Ranked		196.707	199.702	1.01523
	3667	Squared		44025.2	45400.4	1.03124
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	2882	Measured		8175.27	7948.01	1.02859
	2991	Squared		44050.1	45624.8	1.03575
	3126	Measured	High confidence	0.00001	0.00001	1
		Ranked
		Squared
		Rooted

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.