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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 51 to 100 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	Value Type	red	green	network_comparison
15 kda selenoprotein precursor. [swissprot;acc:o60613]	1334	Rooted	64.5959	67.2624	1.04128
	1948	Ranked	214.522	212.432	1.00984
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	2855	Measured	0.00001	0.00001	1
		Ranked
		Squared
		Rooted
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	1051	Ranked	211.449	217.998	1.03097
	2377	Squared	25809.5	27574.1	1.06837
	2521	Measured	5964.17	6113.96	1.02511
	2642	Rooted	63.9773	63.5847	1.00617
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]	1393	Measured	5743.36	6192.72	1.07824
	1463	Rooted	60.3015	62.6331	1.03867
	1593	Squared	29261.2	32473.8	1.10979
	2007	Ranked	225.019	222.969	1.00919
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218]	1160		208.55	214.041	1.02633
	2426	Squared	27135.1	28847.4	1.0631
	2506	Measured	6200.39	6362.25	1.0261
	2700	Rooted	65.3323	65.1252	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]	1484	Ranked	198.927	202.726	1.0191
	1699	Squared	28693.8	31699.9	1.10476
	2451	Measured	6737.15	6957.34	1.03268
	2716	Rooted	69.1013	69.1987	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]	1389	Ranked	218.47	213.875	1.02148
	1579	Rooted	61.9705	64.1938	1.03588
	2288	Measured	5783.76	6048.94	1.04585
	2488	Squared	25184.8	26643.2	1.05791
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	107	Measured	4266.04	5843.51	1.36977
	135	Rooted	54.935	66.6101	1.21253
	183	Ranked	228.306	198.011	1.153
	290	Squared	15734.4	20126.8	1.27916
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]	3079	Measured	0.00001	0.00001	1
		Ranked
		Squared
		Rooted
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	1521	Measured	5938.56	6376.76	1.07379
	1644	Squared	27191.5	30104.4	1.10713
	1870	Rooted	62.901	64.7621	1.02959
	2503	Ranked	215.581	216.137	1.00258
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1496	Squared	27295.8	30410	1.11409
	1527	Measured	5926.76	6362.33	1.07349
	1916	Rooted	62.679	64.4831	1.02878
	2474	Ranked	216.64	217.285	1.00298
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1489	Squared	26277.3	29299.3	1.115
	1567	Measured	5822.25	6242.94	1.07226
	2044	Rooted	62.2342	63.9055	1.02686
	2327	Ranked	217.413	218.426	1.00466
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1481	Squared	26142.6	29163.8	1.11557
	1539	Measured	5783.97	6207.5	1.07322
	1979	Rooted	61.9542	63.6738	1.02776
	2395	Ranked	218.192	219.014	1.00377

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.