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	red	Interaction Map	green	Value Type	network_comparison	Filtered

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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