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

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Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	green	Filtered	Value Type	red	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	245.247	1	Ranked	185.678	1.32082
	37	934.348	0	Measured	334.401	2.79409
		1034.13		Squared	101.05	10.2338
	53	18.0183		Rooted	11.844	1.5213
	60	2765.82	1	Measured	4489.19	1.6231
	64	47.2654		Rooted	63.8686	1.35128
	242	13895.8	0	Ranked	15260.6	1.09822
	245	6768.05	1	Squared	8875.01	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	39351.7			30807.7	1.27733
	509	8630.06		Measured	7551.8	1.14278
	805	79.1513		Rooted	74.3557	1.0645
	1038	181.041		Ranked	186.741	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	39383.9		Squared	30826.5	1.2776
	508	8636.87		Measured	7556.75	1.14293
	804	79.1931		Rooted	74.3877	1.0646
	1032	180.943		Ranked	186.664	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	38866.5		Squared	30566.4	1.27154
	514	8532.02		Measured	7477	1.1411
	822	78.5795		Rooted	73.8577	1.06393
	1048	182.308		Ranked	187.96	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	38919.9		Squared	30596.2	1.27205
	513	8543.66		Measured	7485.08	1.14143
	811	78.6514		Rooted	73.9102	1.06415
	1043	182.137		Ranked	187.834	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	0.00001		Measured	0.00001	1
				Ranked
				Squared
				Rooted
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	588	27879.3		Squared	23526.4	1.18502
	1136	6303.92		Measured	5790.65	1.08864
	1907	65.2789		Rooted	63.4353	1.02906
	1963	213.703		Ranked	211.633	1.00978
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	2922	0.00001		Measured	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	32561.8		Squared	28551.5	1.14046
	1411	6262.07		Measured	5812.02	1.07743
	1943	63.0838		Rooted	61.3337	1.02853
	2439	221.425		Ranked	220.681	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	0.00001		Measured	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	32641.7		Squared	28600.9	1.14128
	1415	6265.44		Measured	5815.33	1.0774
	1961	63.0743		Rooted	61.3419	1.02824
	2396	221.51		Ranked	220.683	1.00375
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	921	29768.2		Squared	25739.7	1.15651
	1600	6788.96		Measured	6336.22	1.07145

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.