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

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Showing element 1 to 50 of 66312 in total

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description	Rank	Value Type	green	Interaction Map	Network Comparison Type	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	Ranked	245.247	High confidence	Divided	185.678	1.32082
	54				Subtracted		59.569
	60	Measured	2765.82		Divided	4489.19	1.6231
	64	Rooted	47.2654			63.8686	1.35128
	67				Subtracted		16.6032
	164	Measured	2765.82			4489.19	1723.37
	245	Squared	6768.05		Divided	8875.01	1.31131
	1119		41688.5	Low confidence		43628.5	1.04654
	1423				Subtracted		1940
	1962		6768.05	High confidence		8875.01	2106.96
	4130	Ranked	201.5	Low confidence	Divided	199.383	1.01062
	4141				Subtracted		2.117
	4909	Measured	7900.54			7853.62	46.92
	4914				Divided		1.00597
		Rooted	72.6287			71.9496	1.00944
	4919				Subtracted		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	Squared	39351.7	High confidence		30807.7	8544
	295				Divided		1.27733
	310	Measured	8630.06		Subtracted	7551.8	1078.26
	509				Divided		1.14278
	610	Rooted	79.1513		Subtracted	74.3557	4.7956
	780	Measured	8585.64	Low confidence		8255.95	329.69
	805	Rooted	79.1513	High confidence	Divided	74.3557	1.0645
	885	Measured	8585.64	Low confidence		8255.95	1.03993
	980	Rooted	76.3375		Subtracted	73.5001	2.8374
	1038	Ranked	181.041	High confidence	Divided	186.741	1.03148
	1092	Rooted	76.3375	Low confidence		73.5001	1.0386
	1120	Ranked	181.041	High confidence	Subtracted	186.741	5.7
	1328		194.038	Low confidence	Divided	198.342	1.02218
	1408				Subtracted		4.304
	4514	Squared	45736			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	High confidence	Subtracted	30826.5	8557.4
	294				Divided		1.2776
	307	Measured	8636.87		Subtracted	7556.75	1080.12
	508				Divided		1.14293
	609	Rooted	79.1931		Subtracted	74.3877	4.8054
	773	Measured	8587.03	Low confidence		8256.68	330.35
	804	Rooted	79.1931	High confidence	Divided	74.3877	1.0646
	880	Measured	8587.03	Low confidence		8256.68	1.04001
	977	Rooted	76.3467		Subtracted	73.5068	2.8399
	1032	Ranked	180.943	High confidence	Divided	186.664	1.03162
	1084	Rooted	76.3467	Low confidence		73.5068	1.03863
	1115	Ranked	180.943	High confidence	Subtracted	186.664	5.721
	1322		194.014	Low confidence	Divided	198.322	1.0222
	1406				Subtracted		4.308
	4523	Squared	45740.5			46616.1	875.6
	4569				Divided		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]	210	Measured	9081.29		Subtracted	8530.51	550.78
	237				Divided		1.06457

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.