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

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Network Comparison Type	Rank	Value Type	green	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Divided	18	Ranked	245.247	185.678	1.32082
		60	Measured	2765.82	4489.19	1.6231
		64	Rooted	47.2654	63.8686	1.35128
		245	Squared	6768.05	8875.01	1.31131
	Subtracted	54	Ranked	245.247	185.678	59.569
		67	Rooted	47.2654	63.8686	16.6032
		164	Measured	2765.82	4489.19	1723.37
		1962	Squared	6768.05	8875.01	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]	Divided	295		39351.7	30807.7	1.27733
		509	Measured	8630.06	7551.8	1.14278
		805	Rooted	79.1513	74.3557	1.0645
		1038	Ranked	181.041	186.741	1.03148
	Subtracted	274	Squared	39351.7	30807.7	8544
		310	Measured	8630.06	7551.8	1078.26
		610	Rooted	79.1513	74.3557	4.7956
		1120	Ranked	181.041	186.741	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]	Divided	294	Squared	39383.9	30826.5	1.2776
		508	Measured	8636.87	7556.75	1.14293
		804	Rooted	79.1931	74.3877	1.0646
		1032	Ranked	180.943	186.664	1.03162
	Subtracted	273	Squared	39383.9	30826.5	8557.4
		307	Measured	8636.87	7556.75	1080.12
		609	Rooted	79.1931	74.3877	4.8054
		1115	Ranked	180.943	186.664	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]	Divided	311	Squared	38866.5	30566.4	1.27154
		514	Measured	8532.02	7477	1.1411
		822	Rooted	78.5795	73.8577	1.06393
		1048	Ranked	182.308	187.96	1.031
	Subtracted	280	Squared	38866.5	30566.4	8300.1
		319	Measured	8532.02	7477	1055.02
		631	Rooted	78.5795	73.8577	4.7218
		1128	Ranked	182.308	187.96	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]	Divided	308	Squared	38919.9	30596.2	1.27205
		513	Measured	8543.66	7485.08	1.14143
		811	Rooted	78.6514	73.9102	1.06415
		1043	Ranked	182.137	187.834	1.03128
	Subtracted	279	Squared	38919.9	30596.2	8323.7
		318	Measured	8543.66	7485.08	1058.58
		616	Rooted	78.6514	73.9102	4.7412
		1121	Ranked	182.137	187.834	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]	Divided	3126	Measured	0.00001	0.00001	1
			Ranked
			Squared
			Rooted
	Subtracted		Measured	0	0	0
			Ranked
			Squared
			Rooted
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	Divided	588	Squared	27879.3	23526.4	1.18502
		1136	Measured	6303.92	5790.65	1.08864

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.