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

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Showing element 101 to 150 of 29840 in total

Filtered  : 1
Interaction Map  : High confidence

description	Value Type	Rank	Network Comparison Type	red	green	network_comparison
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	Squared	786	Subtracted	25739.7	29768.2	4028.5
		921	Divided			1.15651
	Rooted	1933	Subtracted	66.966	68.7832	1.8172
		2036	Divided			1.02714
15 kda selenoprotein precursor. [swissprot;acc:o60613]	Measured	865	Subtracted	6344.41	6933.36	588.95
		1043	Divided			1.09283
	Ranked	1920	Subtracted	214.522	212.432	2.09
		1948	Divided			1.00984
	Squared	590	Subtracted	29772.1	34456.5	4684.4
		914	Divided			1.15734
	Rooted	1304	Subtracted	64.5959	67.2624	2.6665
		1334	Divided			1.04128
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	Measured	2855		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
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	Measured	2496		5964.17	6113.96	149.79
		2521	Divided			1.02511
	Ranked	1029	Subtracted	211.449	217.998	6.549
		1051	Divided			1.03097
	Squared	2200	Subtracted	25809.5	27574.1	1764.6
		2377	Divided			1.06837
	Rooted	2633	Subtracted	63.9773	63.5847	0.3926
		2642	Divided			1.00617
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]	Measured	1393		5743.36	6192.72	1.07824
		1426	Subtracted			449.36
	Ranked	1954		225.019	222.969	2.05
		2007	Divided			1.00919
	Squared	1128	Subtracted	29261.2	32473.8	3212.6
		1593	Divided			1.10979
	Rooted	1463		60.3015	62.6331	1.03867
		1527	Subtracted			2.3316
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218]	Measured	2455		6200.39	6362.25	161.86
		2506	Divided			1.0261
	Ranked	1160		208.55	214.041	1.02633
		1164	Subtracted			5.491
	Squared	2227		27135.1	28847.4	1712.3
		2426	Divided			1.0631
	Rooted	2686	Subtracted	65.3323	65.1252	0.2071
		2700	Divided			1.00318
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]	Measured	2344	Subtracted	6737.15	6957.34	220.19
		2451	Divided			1.03268
	Ranked	1484		198.927	202.726	1.0191
		1515	Subtracted			3.799
	Squared	1230		28693.8	31699.9	3006.1
		1699	Divided			1.10476

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.