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 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Rank	Value Type	green	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	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
	1962			Subtracted		2106.96
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		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
	805			Divided		1.0645
	1038	Ranked	181.041		186.741	1.03148
	1120			Subtracted		5.7
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	Squared	39383.9		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
	804			Divided		1.0646
	1032	Ranked	180.943		186.664	1.03162
	1115			Subtracted		5.721
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]	280	Squared	38866.5		30566.4	8300.1
	311			Divided		1.27154
	319	Measured	8532.02	Subtracted	7477	1055.02
	514			Divided		1.1411
	631	Rooted	78.5795	Subtracted	73.8577	4.7218
	822			Divided		1.06393
	1048	Ranked	182.308		187.96	1.031
	1128			Subtracted		5.652
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]	279	Squared	38919.9		30596.2	8323.7
	308			Divided		1.27205
	318	Measured	8543.66	Subtracted	7485.08	1058.58
	513			Divided		1.14143
	616	Rooted	78.6514	Subtracted	73.9102	4.7412
	811			Divided		1.06415
	1043	Ranked	182.137		187.834	1.03128
	1121			Subtracted		5.697
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]	3126	Measured	0		0	0
			0.00001	Divided	0.00001	1
		Ranked	0	Subtracted	0	0
			0.00001	Divided	0.00001	1
		Squared	0	Subtracted	0	0
			0.00001	Divided	0.00001	1
		Rooted	0	Subtracted	0	0
			0.00001	Divided	0.00001	1
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	588	Squared	27879.3		23526.4	1.18502
	688			Subtracted		4352.9

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.