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

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Showing element 401 to 450 of 77072 in total

description	Filtered	Rank	Value Type	Network Comparison Type	green	Interaction Map	red	network_comparison
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	0	19	Measured	Divided	26.1599	High confidence	305.45	11.6763
		26	Squared		0.344399		44.3683	128.828
			Rooted		3.80565		13.7805	3.62106
		28	Ranked	Subtracted	18499.2		12941.7	5557.5
			Rooted		3.80565		13.7805	9.97485
		47	Ranked	Divided	18499.2		12941.7	1.42943
		115	Measured	Subtracted	26.1599		305.45	279.29
		131	Rooted	Divided	9.42485	Low confidence	11.365	1.20585
		171	Measured		181.734		222.779	1.22585
		220	Ranked	Subtracted	14695.2		13533.1	1162.1
		336	Squared		0.344399	High confidence	44.3683	44.0239
		376	Rooted		9.42485	Low confidence	11.365	1.94015
		384	Ranked	Divided	14695.2		13533.1	1.08587
		635	Measured	Subtracted	181.734		222.779	41.045
		697	Squared	Divided	296.481		307.765	1.03806
		749		Subtracted				11.284
	1	13	Rooted	Divided	52.5277		39.2301	1.33896
		14	Ranked	Subtracted	238.476		286.396	47.92
		19	Measured	Divided	3915.4		3032.56	1.29112
		25	Ranked		238.476		286.396	1.20094
		26	Rooted	Subtracted	52.5277		39.2301	13.2976
		107	Measured		3915.4		3032.56	882.84
		3079		Divided	0.00001	High confidence	0.00001	1
				Subtracted	0		0	0
			Ranked	Divided	0.00001		0.00001	1
				Subtracted	0		0	0
			Squared	Divided	0.00001		0.00001	1
				Subtracted	0		0	0
			Rooted	Divided	0.00001		0.00001	1
				Subtracted	0		0	0
		4834	Squared	Divided	15383	Low confidence	15514.2	1.00853
		4965		Subtracted				131.2
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]		1297			30104.4	High confidence	27191.5	2912.9
		1491	Measured		6376.76		5938.56	438.2
		1521		Divided				1.07379
		1644	Squared		30104.4		27191.5	1.10713
		1677	Measured	Subtracted	8422.67	Low confidence	8156.56	266.11
		1870	Rooted	Divided	64.7621	High confidence	62.901	1.02959
		1881	Measured		8422.67	Low confidence	8156.56	1.03263
		1883	Rooted	Subtracted	64.7621	High confidence	62.901	1.8611
		2386			75.2485	Low confidence	72.8011	2.4474
		2496		Divided				1.03362
		2497	Ranked	Subtracted	216.137	High confidence	215.581	0.556
		2503		Divided				1.00258
		2962			196.692	Low confidence	200.017	1.0169
		2968		Subtracted				3.325
		4226	Squared		45383.5		46486	1102.5
		4304		Divided				1.02429
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]		1181		Subtracted	30410	High confidence	27295.8	3114.2
		1496		Divided				1.11409

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.