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	Rank	Interaction Map	green	Network Comparison Type	red	Filtered	network_comparison

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Showing element 1 to 50 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

description	Value Type	Rank	green	red	Filtered	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	37	934.348	334.401	0	2.79409
		60	2765.82	4489.19	1	1.6231
	Ranked	18	245.247	185.678		1.32082
		242	13895.8	15260.6	0	1.09822
	Squared	37	1034.13	101.05		10.2338
		245	6768.05	8875.01	1	1.31131
	Rooted	53	18.0183	11.844	0	1.5213
		64	47.2654	63.8686	1	1.35128
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	509	8630.06	7551.8		1.14278
	Ranked	1038	181.041	186.741		1.03148
	Squared	295	39351.7	30807.7		1.27733
	Rooted	805	79.1513	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	508	8636.87	7556.75		1.14293
	Ranked	1032	180.943	186.664		1.03162
	Squared	294	39383.9	30826.5		1.2776
	Rooted	804	79.1931	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	514	8532.02	7477		1.1411
	Ranked	1048	182.308	187.96		1.031
	Squared	311	38866.5	30566.4		1.27154
	Rooted	822	78.5795	73.8577		1.06393
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	513	8543.66	7485.08		1.14143
	Ranked	1043	182.137	187.834		1.03128
	Squared	308	38919.9	30596.2		1.27205
	Rooted	811	78.6514	73.9102		1.06415
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]	Measured	3126	0.00001	0.00001		1
	Ranked
	Squared
	Rooted
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	Measured	1136	6303.92	5790.65		1.08864
	Ranked	1963	213.703	211.633		1.00978
	Squared	588	27879.3	23526.4		1.18502
	Rooted	1907	65.2789	63.4353		1.02906
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	Measured	2922	0.00001	0.00001		1
	Ranked
	Squared
	Rooted
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	Measured	1411	6262.07	5812.02		1.07743
	Ranked	2439	221.425	220.681		1.00337
	Squared	1143	32561.8	28551.5		1.14046
	Rooted	1943	63.0838	61.3337		1.02853
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]	Measured	3088	0.00001	0.00001		1
	Ranked
	Squared
	Rooted
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	Measured	1415	6265.44	5815.33		1.0774
	Ranked	2396	221.51	220.683		1.00375
	Squared	1135	32641.7	28600.9		1.14128
	Rooted	1961	63.0743	61.3419		1.02824
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	Measured	1600	6788.96	6336.22		1.07145
	Ranked	2366	202.529	203.353		1.00407

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.