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

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Showing element 151 to 200 of 29840 in total

Interaction Map  : High confidence

description	Rank	Value Type	Filtered	Network Comparison Type	green	red	network_comparison
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]	2715	Rooted	1	Subtracted	69.1987	69.1013	0.0974
	2716			Divided			1.00141
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]	1336	Ranked		Subtracted	213.875	218.47	4.595
	1389			Divided			1.02148
	1579	Rooted			64.1938	61.9705	1.03588
	1619			Subtracted			2.2233
	2239	Measured			6048.94	5783.76	265.18
	2288			Divided			1.04585
	2327	Squared		Subtracted	26643.2	25184.8	1458.4
	2488			Divided			1.05791
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	107	Measured			5843.51	4266.04	1.36977
	135	Rooted			66.6101	54.935	1.21253
	140	Ranked		Subtracted	198.011	228.306	30.295
	163	Rooted			66.6101	54.935	11.6751
	179	Measured			5843.51	4266.04	1577.47
	183	Ranked		Divided	198.011	228.306	1.153
	290	Squared			20126.8	15734.4	1.27916
	650			Subtracted			4392.4
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]	19	Measured	0	Divided	26.1599	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
	336	Squared			0.344399	44.3683	44.0239
	3079	Measured	1	Divided	0.00001	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
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	1297	Squared			30104.4	27191.5	2912.9
	1491	Measured			6376.76	5938.56	438.2
	1521			Divided			1.07379
	1644	Squared			30104.4	27191.5	1.10713
	1870	Rooted			64.7621	62.901	1.02959
	1883			Subtracted			1.8611
	2497	Ranked			216.137	215.581	0.556
	2503			Divided			1.00258
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1181	Squared		Subtracted	30410	27295.8	3114.2
	1496			Divided			1.11409
	1511	Measured		Subtracted	6362.33	5926.76	435.57
	1527			Divided			1.07349
	1916	Rooted			64.4831	62.679	1.02878
	1949			Subtracted			1.8041
	2466	Ranked			217.285	216.64	0.645
	2474			Divided			1.00298

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.