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

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description	Rank	Value Type	Interaction Map	Network Comparison Type	green	red	network_comparison
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664]	3986	Rooted	Low confidence	Subtracted	74.6723	72.7042	1.9681
	4018			Divided			1.02707
	4587	Measured		Subtracted	8354	8218.07	135.93
	4609			Divided			1.01654
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880]	1636	Squared			40720.1	42455.4	1.04262
	2121			Subtracted			1735.3
	2443	Measured		Divided	7708.55	7480.51	1.03048
	2870			Subtracted			228.04
	3647	Rooted		Divided	71.2917	69.2456	1.02955
	3828			Subtracted			2.0461
	4270	Ranked			205.097	207	1.903
	4455			Divided			1.00928
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]	870			Subtracted	201.99	207.026	5.036
	930	Rooted		Divided	72.6721	69.8925	1.03977
	941	Ranked			201.99	207.026	1.02493
	1089	Rooted		Subtracted	72.6721	69.8925	2.7796
	1128	Squared	High confidence		32473.8	29261.2	3212.6
	1393	Measured		Divided	6192.72	5743.36	1.07824
	1426			Subtracted			449.36
	1463	Rooted		Divided	62.6331	60.3015	1.03867
	1493	Squared	Low confidence		42254.4	44097.2	1.04361
	1527	Rooted	High confidence	Subtracted	62.6331	60.3015	2.3316
	1593	Squared		Divided	32473.8	29261.2	1.10979
	1733		Low confidence	Subtracted	42254.4	44097.2	1842.8
	1954	Ranked	High confidence		222.969	225.019	2.05
	1973	Measured	Low confidence	Divided	7938.52	7690.22	1.03229
	2007	Ranked	High confidence		222.969	225.019	1.00919
	2251	Measured	Low confidence	Subtracted	7938.52	7690.22	248.3
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218]	869	Rooted		Divided	75.0085	72.1119	1.04017
	884			Subtracted			2.8966
	992	Ranked			196.729	201.562	4.833
	994			Divided			1.02457
	1019	Measured		Subtracted	8332.97	8029.13	303.84
	1032			Divided			1.03784
	1160	Ranked	High confidence		214.041	208.55	1.02633
	1164			Subtracted			5.491
	2227	Squared			28847.4	27135.1	1712.3
	2426			Divided			1.0631
	2455	Measured		Subtracted	6362.25	6200.39	161.86
	2506			Divided			1.0261
	2686	Rooted		Subtracted	65.1252	65.3323	0.2071
	2700			Divided			1.00318
	3934	Squared	Low confidence	Subtracted	44259.3	45494.3	1235
	4027			Divided			1.0279
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]	1230		High confidence	Subtracted	31699.9	28693.8	3006.1
	1484	Ranked		Divided	202.726	198.927	1.0191
	1515			Subtracted			3.799
	1699	Squared		Divided	31699.9	28693.8	1.10476
	2344	Measured		Subtracted	6957.34	6737.15	220.19
	2451			Divided			1.03268

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.