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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0

description	green	Rank	red	Value Type	Interaction Map	network_comparison	Network Comparison Type
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	17.0804	537	16.298	Rooted	Low confidence	1.04801	Divided
		634				0.7824	Subtracted
	18.0183	53	11.844		High confidence	1.5213	Divided
		69				6.1743	Subtracted
	851.77	131	645.504	Measured	Low confidence	1.31954	Divided
		273				206.266	Subtracted
	934.348	37	334.401		High confidence	2.79409	Divided
		45				599.947	Subtracted
	1034.13	37	101.05	Squared		10.2338	Divided
		131				933.08	Subtracted
	1268.51	146	775.72		Low confidence	1.63527	Divided
		319				492.79	Subtracted
	13590.3	600	13205.3	Ranked		385
		629				1.02915	Divided
	13895.8	172	15260.6		High confidence	1364.8	Subtracted
		242				1.09822	Divided
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	39.5126	726	39.0982	Rooted	Low confidence	0.4144	Subtracted
		768				1.0106	Divided
	4869.42	627	4825.89	Measured		43.53	Subtracted
		778				1.00902	Divided
	10050.9	627	10347.7	Ranked		1.02953
		641				296.8	Subtracted
	40451	536	40270.8	Squared		180.2
		815				1.00447	Divided
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]	0.344399	26	44.3683		High confidence	128.828
		336				44.0239	Subtracted
	3.80565	26	13.7805	Rooted		3.62106	Divided
		28				9.97485	Subtracted
	9.42485	131	11.365		Low confidence	1.20585	Divided
		376				1.94015	Subtracted
	26.1599	19	305.45	Measured	High confidence	11.6763	Divided
		115				279.29	Subtracted
	181.734	171	222.779		Low confidence	1.22585	Divided
		635				41.045	Subtracted
	296.481	697	307.765	Squared		1.03806	Divided
		749				11.284	Subtracted
	14695.2	220	13533.1	Ranked		1162.1
		384				1.08587	Divided
	18499.2	28	12941.7		High confidence	5557.5	Subtracted
		47				1.42943	Divided
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	23.2445	793	23.11	Rooted	Low confidence	1.00582
		797				0.1345	Subtracted
	32.0298	335	30.7424		High confidence	1.2874
		370				1.04188	Divided
	1609.88	762	1593.68	Measured	Low confidence	16.2	Subtracted
		771				1.01017	Divided
	2642.79	380	2683.61		High confidence	40.82	Subtracted
		451				1.01545	Divided
	6490.54	584	6603.33	Squared	Low confidence	112.79	Subtracted
		763				1.01738	Divided

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.