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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.