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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

description	Value Type	Interaction Map	Rank	green	network_comparison	Filtered	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	High confidence	37	934.348	2.79409	0	334.401
			60	2765.82	1.6231	1	4489.19
		Low confidence	131	851.77	1.31954	0	645.504
			4914	7900.54	1.00597	1	7853.62
	Ranked	High confidence	18	245.247	1.32082		185.678
			242	13895.8	1.09822	0	15260.6
		Low confidence	629	13590.3	1.02915		13205.3
			4130	201.5	1.01062	1	199.383
	Squared	High confidence	37	1034.13	10.2338	0	101.05
			245	6768.05	1.31131	1	8875.01
		Low confidence	146	1268.51	1.63527	0	775.72
			1119	41688.5	1.04654	1	43628.5
	Rooted	High confidence	53	18.0183	1.5213	0	11.844
			64	47.2654	1.35128	1	63.8686
		Low confidence	537	17.0804	1.04801	0	16.298
			4914	72.6287	1.00944	1	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	High confidence	509	8630.06	1.14278		7551.8
		Low confidence	885	8585.64	1.03993		8255.95
	Ranked	High confidence	1038	181.041	1.03148		186.741
		Low confidence	1328	194.038	1.02218		198.342
	Squared	High confidence	295	39351.7	1.27733		30807.7
		Low confidence	4562	45736	1.01928		46617.7
	Rooted	High confidence	805	79.1513	1.0645		74.3557
		Low confidence	1092	76.3375	1.0386		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	High confidence	508	8636.87	1.14293		7556.75
		Low confidence	880	8587.03	1.04001		8256.68
	Ranked	High confidence	1032	180.943	1.03162		186.664
		Low confidence	1322	194.014	1.0222		198.322
	Squared	High confidence	294	39383.9	1.2776		30826.5
		Low confidence	4569	45740.5	1.01914		46616.1
	Rooted	High confidence	804	79.1931	1.0646		74.3877
		Low confidence	1084	76.3467	1.03863		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	High confidence	514	8532.02	1.1411		7477
		Low confidence	237	9081.29	1.06457		8530.51
	Ranked	High confidence	1048	182.308	1.031		187.96
		Low confidence	588	185.859	1.03039		191.507
	Squared	High confidence	311	38866.5	1.27154		30566.4
		Low confidence	4138	47372.8	1.02676		46138.2
	Rooted	High confidence	822	78.5795	1.06393		73.8577
		Low confidence	378	79.5804	1.04871		75.8843
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	High confidence	513	8543.66	1.14143		7485.08
		Low confidence	252	9018.94	1.06194		8492.92
	Ranked	High confidence	1043	182.137	1.03128		187.834
		Low confidence	637	186.751	1.029		192.166
	Squared	High confidence	308	38919.9	1.27205		30596.2
		Low confidence	4418	47088.3	1.02256		46049.4
	Rooted	High confidence	811	78.6514	1.06415		73.9102
		Low confidence	427	79.1997	1.04731		75.6219
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	Measured		2035	8323.04	1.03199		8065.05
	Ranked		3423	196.707	1.01523		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.