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	Filtered	Interaction Map	Value Type	Network Comparison Type	green	network_comparison	red

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Showing element 3180 to 3229 of 77072 in total

description	Rank	Filtered	Interaction Map	Value Type	Network Comparison Type	green	network_comparison	red
60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	1255	1	Low confidence	Measured	Subtracted	8101.14	283.76	7817.38
	1501		High confidence	Squared	Divided	20672	1.11407	18555.4
	1696			Rooted		54.8538	1.03286	56.6562
	1829		Low confidence			73.5542	1.03548	71.0339
	1948		High confidence	Squared	Subtracted	20672	2116.6	18555.4
	1950			Rooted		54.8538	1.8024	56.6562
	2048		Low confidence			73.5542	2.5203	71.0339
	2548		High confidence	Measured	Divided	4824.4	1.02087	4725.79
	2569				Subtracted		98.61
	3117		Low confidence	Ranked		200.191	3.237	203.428
	3174				Divided		1.01617
	4198			Squared		42999.9	1.02592	44114.5
	4203				Subtracted		1114.6
60s ribosomal protein l37a. [swissprot;acc:p12751]	18	0	High confidence	Measured	Divided	26.1599	11.6763	305.45
	25			Squared		0.344399	128.828	44.3683
				Rooted		3.80565	3.62106	13.7805
	27			Ranked	Subtracted	18499.2	5557.5	12941.7
				Rooted		3.80565	9.97485	13.7805
	37		Low confidence	Ranked		15783.5	3409.2	12374.3
	41			Rooted		9.96201	6.15969	16.1217
	46		High confidence	Ranked	Divided	18499.2	1.42943	12941.7
	53	1	Low confidence		Subtracted	217.005	22.687	239.692
	54	0		Rooted	Divided	9.96201	1.61832	16.1217
	55	1				64.3669	1.12402	57.2649
	63	0		Ranked		15783.5	1.27551	12374.3
	68	1				217.005	1.10455	239.692
				Rooted	Subtracted	64.3669	7.102	57.2649
	101	0		Measured	Divided	362.955	1.47569	535.61
	114		High confidence		Subtracted	26.1599	279.29	305.45
	139	1	Low confidence		Divided	6277.91	1.08946	5762.4
	244				Subtracted		515.51
	301	0				362.955	172.655	535.61
	335		High confidence	Squared		0.344399	44.0239	44.3683
	680		Low confidence			1009.55	42.95	1052.5
	684				Divided		1.04254
	2959	1	High confidence	Measured		0.00001	1	0.00001
					Subtracted	0	0	0
				Ranked	Divided	0.00001	1	0.00001
					Subtracted	0	0	0
				Squared	Divided	0.00001	1	0.00001
					Subtracted	0	0	0
				Rooted	Divided	0.00001	1	0.00001
					Subtracted	0	0	0
	3873		Low confidence	Squared	Divided	31052	1.02957	31970.2
	4479				Subtracted		918.2
60s ribosomal protein l38. [swissprot;acc:p23411]	2612			Measured	Divided	8146.53	1.0299	7910.01
	2613				Subtracted		236.52
	2985			Squared		43366.8	1534.6	44901.4
	3043				Divided		1.03539
	3566			Rooted		73.6472	1.02984	71.5134

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.