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

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Showing element 1 to 50 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	green	Rank	Value Type	Interaction Map	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	47.2654	64	Rooted	High confidence	63.8686	1.35128
	72.6287	4914		Low confidence	71.9496	1.00944
	201.5	4130	Ranked		199.383	1.01062
	245.247	18		High confidence	185.678	1.32082
	2765.82	60	Measured		4489.19	1.6231
	6768.05	245	Squared		8875.01	1.31131
	7900.54	4914	Measured	Low confidence	7853.62	1.00597
	41688.5	1119	Squared		43628.5	1.04654
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]	76.3375	1092	Rooted		73.5001	1.0386
	79.1513	805		High confidence	74.3557	1.0645
	181.041	1038	Ranked		186.741	1.03148
	194.038	1328		Low confidence	198.342	1.02218
	8585.64	885	Measured		8255.95	1.03993
	8630.06	509		High confidence	7551.8	1.14278
	39351.7	295	Squared		30807.7	1.27733
	45736	4562		Low confidence	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]	76.3467	1084	Rooted		73.5068	1.03863
	79.1931	804		High confidence	74.3877	1.0646
	180.943	1032	Ranked		186.664	1.03162
	194.014	1322		Low confidence	198.322	1.0222
	8587.03	880	Measured		8256.68	1.04001
	8636.87	508		High confidence	7556.75	1.14293
	39383.9	294	Squared		30826.5	1.2776
	45740.5	4569		Low confidence	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]	78.5795	822	Rooted	High confidence	73.8577	1.06393
	79.5804	378		Low confidence	75.8843	1.04871
	182.308	1048	Ranked	High confidence	187.96	1.031
	185.859	588		Low confidence	191.507	1.03039
	8532.02	514	Measured	High confidence	7477	1.1411
	9081.29	237		Low confidence	8530.51	1.06457
	38866.5	311	Squared	High confidence	30566.4	1.27154
	47372.8	4138		Low confidence	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]	78.6514	811	Rooted	High confidence	73.9102	1.06415
	79.1997	427		Low confidence	75.6219	1.04731
	182.137	1043	Ranked	High confidence	187.834	1.03128
	186.751	637		Low confidence	192.166	1.029
	8543.66	513	Measured	High confidence	7485.08	1.14143
	9018.94	252		Low confidence	8492.92	1.06194
	38919.9	308	Squared	High confidence	30596.2	1.27205
	47088.3	4418		Low confidence	46049.4	1.02256
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	74.9741	2766	Rooted		72.5914	1.03282
	196.707	3423	Ranked		199.702	1.01523
	8323.04	2035	Measured		8065.05	1.03199
	44025.2	3667	Squared		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]	0.00001	3126	Measured	High confidence	0.00001	1
			Ranked
			Squared
			Rooted
	73.847	3189		Low confidence	71.5946	1.03146
	199.628	3585	Ranked		202.517	1.01447

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.