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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

description	Value Type	Filtered	green	Rank	Interaction Map	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	0	851.77	131	Low confidence	645.504	1.31954
			934.348	37	High confidence	334.401	2.79409
		1	2765.82	60		4489.19	1.6231
			7900.54	4914	Low confidence	7853.62	1.00597
	Ranked	0	13590.3	629		13205.3	1.02915
			13895.8	242	High confidence	15260.6	1.09822
		1	201.5	4130	Low confidence	199.383	1.01062
			245.247	18	High confidence	185.678	1.32082
	Squared	0	1034.13	37		101.05	10.2338
			1268.51	146	Low confidence	775.72	1.63527
		1	6768.05	245	High confidence	8875.01	1.31131
			41688.5	1119	Low confidence	43628.5	1.04654
	Rooted	0	17.0804	537		16.298	1.04801
			18.0183	53	High confidence	11.844	1.5213
		1	47.2654	64		63.8686	1.35128
			72.6287	4914	Low confidence	71.9496	1.00944
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]	Measured		8585.64	885		8255.95	1.03993
			8630.06	509	High confidence	7551.8	1.14278
	Ranked		181.041	1038		186.741	1.03148
			194.038	1328	Low confidence	198.342	1.02218
	Squared		39351.7	295	High confidence	30807.7	1.27733
			45736	4562	Low confidence	46617.7	1.01928
	Rooted		76.3375	1092		73.5001	1.0386
			79.1513	805	High confidence	74.3557	1.0645
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]	Measured		8587.03	880	Low confidence	8256.68	1.04001
			8636.87	508	High confidence	7556.75	1.14293
	Ranked		180.943	1032		186.664	1.03162
			194.014	1322	Low confidence	198.322	1.0222
	Squared		39383.9	294	High confidence	30826.5	1.2776
			45740.5	4569	Low confidence	46616.1	1.01914
	Rooted		76.3467	1084		73.5068	1.03863
			79.1931	804	High confidence	74.3877	1.0646
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]	Measured		8532.02	514		7477	1.1411
			9081.29	237	Low confidence	8530.51	1.06457
	Ranked		182.308	1048	High confidence	187.96	1.031
			185.859	588	Low confidence	191.507	1.03039
	Squared		38866.5	311	High confidence	30566.4	1.27154
			47372.8	4138	Low confidence	46138.2	1.02676
	Rooted		78.5795	822	High confidence	73.8577	1.06393
			79.5804	378	Low confidence	75.8843	1.04871
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]	Measured		8543.66	513	High confidence	7485.08	1.14143
			9018.94	252	Low confidence	8492.92	1.06194
	Ranked		182.137	1043	High confidence	187.834	1.03128
			186.751	637	Low confidence	192.166	1.029
	Squared		38919.9	308	High confidence	30596.2	1.27205
			47088.3	4418	Low confidence	46049.4	1.02256
	Rooted		78.6514	811	High confidence	73.9102	1.06415
			79.1997	427	Low confidence	75.6219	1.04731
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	Measured		8323.04	2035		8065.05	1.03199
	Ranked		196.707	3423		199.702	1.01523

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.