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	Interaction Map	Filtered	Network Comparison Type	red	green	network_comparison

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Showing element 1 to 50 of 12912 in total

Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided

description	Rank	Value Type	red	green	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	Ranked	185.678	245.247	1.32082
	60	Measured	4489.19	2765.82	1.6231
	64	Rooted	63.8686	47.2654	1.35128
	245	Squared	8875.01	6768.05	1.31131
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		30807.7	39351.7	1.27733
	509	Measured	7551.8	8630.06	1.14278
	805	Rooted	74.3557	79.1513	1.0645
	1038	Ranked	186.741	181.041	1.03148
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	Squared	30826.5	39383.9	1.2776
	508	Measured	7556.75	8636.87	1.14293
	804	Rooted	74.3877	79.1931	1.0646
	1032	Ranked	186.664	180.943	1.03162
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]	311	Squared	30566.4	38866.5	1.27154
	514	Measured	7477	8532.02	1.1411
	822	Rooted	73.8577	78.5795	1.06393
	1048	Ranked	187.96	182.308	1.031
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]	308	Squared	30596.2	38919.9	1.27205
	513	Measured	7485.08	8543.66	1.14143
	811	Rooted	73.9102	78.6514	1.06415
	1043	Ranked	187.834	182.137	1.03128
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]	3126	Measured	0.00001	0.00001	1
		Ranked
		Squared
		Rooted
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	588	Squared	23526.4	27879.3	1.18502
	1136	Measured	5790.65	6303.92	1.08864
	1907	Rooted	63.4353	65.2789	1.02906
	1963	Ranked	211.633	213.703	1.00978
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	2922	Measured	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]	1143	Squared	28551.5	32561.8	1.14046
	1411	Measured	5812.02	6262.07	1.07743
	1943	Rooted	61.3337	63.0838	1.02853
	2439	Ranked	220.681	221.425	1.00337
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]	3088	Measured	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]	1135	Squared	28600.9	32641.7	1.14128
	1415	Measured	5815.33	6265.44	1.0774
	1961	Rooted	61.3419	63.0743	1.02824
	2396	Ranked	220.683	221.51	1.00375
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	921	Squared	25739.7	29768.2	1.15651
	1600	Measured	6336.22	6788.96	1.07145
	2036	Rooted	66.966	68.7832	1.02714
	2366	Ranked	203.353	202.529	1.00407
15 kda selenoprotein precursor. [swissprot;acc:o60613]	914	Squared	29772.1	34456.5	1.15734
	1043	Measured	6344.41	6933.36	1.09283

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.