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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

description	Rank	Value Type	Filtered	green	Interaction Map	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	Ranked	1	245.247	High confidence	185.678	1.32082
	37	Measured	0	934.348		334.401	2.79409
		Squared		1034.13		101.05	10.2338
	53	Rooted		18.0183		11.844	1.5213
	60	Measured	1	2765.82		4489.19	1.6231
	64	Rooted		47.2654		63.8686	1.35128
	131	Measured	0	851.77	Low confidence	645.504	1.31954
	146	Squared		1268.51		775.72	1.63527
	242	Ranked		13895.8	High confidence	15260.6	1.09822
	245	Squared	1	6768.05		8875.01	1.31131
	537	Rooted	0	17.0804	Low confidence	16.298	1.04801
	629	Ranked		13590.3		13205.3	1.02915
	1119	Squared	1	41688.5		43628.5	1.04654
	4130	Ranked		201.5		199.383	1.01062
	4914	Measured		7900.54		7853.62	1.00597
		Rooted		72.6287		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]	295	Squared		39351.7	High confidence	30807.7	1.27733
	509	Measured		8630.06		7551.8	1.14278
	805	Rooted		79.1513		74.3557	1.0645
	885	Measured		8585.64	Low confidence	8255.95	1.03993
	1038	Ranked		181.041	High confidence	186.741	1.03148
	1092	Rooted		76.3375	Low confidence	73.5001	1.0386
	1328	Ranked		194.038		198.342	1.02218
	4562	Squared		45736		46617.7	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]	294			39383.9	High confidence	30826.5	1.2776
	508	Measured		8636.87		7556.75	1.14293
	804	Rooted		79.1931		74.3877	1.0646
	880	Measured		8587.03	Low confidence	8256.68	1.04001
	1032	Ranked		180.943	High confidence	186.664	1.03162
	1084	Rooted		76.3467	Low confidence	73.5068	1.03863
	1322	Ranked		194.014		198.322	1.0222
	4569	Squared		45740.5		46616.1	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]	237	Measured		9081.29		8530.51	1.06457
	311	Squared		38866.5	High confidence	30566.4	1.27154
	378	Rooted		79.5804	Low confidence	75.8843	1.04871
	514	Measured		8532.02	High confidence	7477	1.1411
	588	Ranked		185.859	Low confidence	191.507	1.03039
	822	Rooted		78.5795	High confidence	73.8577	1.06393
	1048	Ranked		182.308		187.96	1.031
	4138	Squared		47372.8	Low confidence	46138.2	1.02676
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]	252	Measured		9018.94		8492.92	1.06194
	308	Squared		38919.9	High confidence	30596.2	1.27205
	427	Rooted		79.1997	Low confidence	75.6219	1.04731
	513	Measured		8543.66	High confidence	7485.08	1.14143
	637	Ranked		186.751	Low confidence	192.166	1.029
	811	Rooted		78.6514	High confidence	73.9102	1.06415
	1043	Ranked		182.137		187.834	1.03128
	4418	Squared		47088.3	Low confidence	46049.4	1.02256
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	2035	Measured		8323.04		8065.05	1.03199
	2766	Rooted		74.9741		72.5914	1.03282

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.