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

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Showing element 1 to 50 of 77072 in total

description	Rank	green	Network Comparison Type	Value Type	Filtered	Interaction Map	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	245.247	Divided	Ranked	1	High confidence	185.678	1.32082
	37	934.348		Measured	0		334.401	2.79409
		1034.13		Squared			101.05	10.2338
	45	934.348	Subtracted	Measured			334.401	599.947
	53	18.0183	Divided	Rooted			11.844	1.5213
	54	245.247	Subtracted	Ranked	1		185.678	59.569
	60	2765.82	Divided	Measured			4489.19	1.6231
	64	47.2654		Rooted			63.8686	1.35128
	67		Subtracted					16.6032
	69	18.0183			0		11.844	6.1743
	131	851.77	Divided	Measured		Low confidence	645.504	1.31954
		1034.13	Subtracted	Squared		High confidence	101.05	933.08
	146	1268.51	Divided			Low confidence	775.72	1.63527
	164	2765.82	Subtracted	Measured	1	High confidence	4489.19	1723.37
	172	13895.8		Ranked	0		15260.6	1364.8
	242		Divided					1.09822
	245	6768.05		Squared	1		8875.01	1.31131
	273	851.77	Subtracted	Measured	0	Low confidence	645.504	206.266
	319	1268.51		Squared			775.72	492.79
	537	17.0804	Divided	Rooted			16.298	1.04801
	600	13590.3	Subtracted	Ranked			13205.3	385
	629		Divided					1.02915
	634	17.0804	Subtracted	Rooted			16.298	0.7824
	1119	41688.5	Divided	Squared	1		43628.5	1.04654
	1423		Subtracted					1940
	1962	6768.05				High confidence	8875.01	2106.96
	4130	201.5	Divided	Ranked		Low confidence	199.383	1.01062
	4141		Subtracted					2.117
	4909	7900.54		Measured			7853.62	46.92
	4914	72.6287	Divided	Rooted			71.9496	1.00944
		7900.54		Measured			7853.62	1.00597
	4919	72.6287	Subtracted	Rooted			71.9496	0.6791
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]	274	39351.7		Squared		High confidence	30807.7	8544
	295		Divided					1.27733
	310	8630.06	Subtracted	Measured			7551.8	1078.26
	509		Divided					1.14278
	610	79.1513	Subtracted	Rooted			74.3557	4.7956
	780	8585.64		Measured		Low confidence	8255.95	329.69
	805	79.1513	Divided	Rooted		High confidence	74.3557	1.0645
	885	8585.64		Measured		Low confidence	8255.95	1.03993
	980	76.3375	Subtracted	Rooted			73.5001	2.8374
	1038	181.041	Divided	Ranked		High confidence	186.741	1.03148
	1092	76.3375		Rooted		Low confidence	73.5001	1.0386
	1120	181.041	Subtracted	Ranked		High confidence	186.741	5.7
	1328	194.038	Divided			Low confidence	198.342	1.02218
	1408		Subtracted					4.304
	4514	45736		Squared			46617.7	881.7
	4562		Divided					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]	273	39383.9	Subtracted			High confidence	30826.5	8557.4
	294		Divided					1.2776

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.