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	green	Interaction Map	Network Comparison Type	Filtered	red	network_comparison

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Showing element 1001 to 1050 of 66312 in total

Filtered  : 1

description	Rank	Value Type	green	Interaction Map	Network Comparison Type	red	network_comparison
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]	915	Ranked	199.196	Low confidence	Subtracted	204.147	4.951
	950				Divided		1.02485
	960	Rooted	65.1892	High confidence	Subtracted	61.6649	3.5243
	972				Divided		1.05715
	1041	Ranked	213.685		Subtracted	220.118	6.433
	1084				Divided		1.03011
	1143	Rooted	73.8482	Low confidence		71.1233	1.03831
	1232				Subtracted		2.7249
	1245	Measured	6371.14	High confidence		5885	486.14
	1275				Divided		1.08261
	1627	Squared	43316.1	Low confidence		45165.2	1.04269
	1710				Subtracted		1849.1
	2090	Measured	8138.17		Divided	7887.47	1.03178
	2168				Subtracted		250.7
	2527	Squared	30015.7	High confidence		28935	1080.7
	2610				Divided		1.03735
3-oxo-5-beta-steroid 4-dehydrogenase (ec 1.3.99.6) (delta(4)-3- ketosteroid 5-beta-reductase) (aldo-keto reductase family 1 member d1). [swissprot;acc:p51857]	1896	Ranked	197.384	Low confidence	Subtracted	201.286	3.902
	1902				Divided		1.01977
	1945	Rooted	74.9328		Subtracted	72.3967	2.5361
	2018				Divided		1.03503
	2075	Measured	8361.72		Subtracted	8107.73	253.99
	2235				Divided		1.03133
	2942	Squared	44839.4		Subtracted	46389.7	1550.3
	3174				Divided		1.03457
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	739	Ranked	283.472	High confidence	Subtracted	272.878	10.594
	897				Divided		1.03882
	2394	Rooted	42.7253			43.4014	1.01582
	2500				Subtracted		0.6761
	2513	Squared	42545.5	Low confidence	Divided	44180.9	1.03844
	2531				Subtracted		1635.4
	2547	Measured	3444.18	High confidence	Divided	3370.46	1.02187
	2627				Subtracted		73.72
	2650	Squared	16197		Divided	16658.1	1.02847
	2675				Subtracted		461.1
	3553	Measured	7932.5	Low confidence	Divided	7733.78	1.0257
	3653				Subtracted		198.72
	4104	Rooted	71.9424		Divided	70.109	1.02615
	4323				Subtracted		1.8334
	4759	Ranked	205.83			206.842	1.012
	4765				Divided		1.00492
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	116	Squared	45948.1			52687.3	1.14667
	138				Subtracted		6739.2
	1714	Rooted	69.9589	High confidence		67.8897	2.0692
	1826				Divided		1.03048
	1839	Ranked	207.631	Low confidence	Subtracted	203.696	3.935
	2068				Divided		1.01932
	2133	Measured	6786.23	High confidence	Subtracted	6486.84	299.39
	2261				Divided		1.04615
	2358	Ranked	197.346			198.181	1.00423
	2385				Subtracted		0.835

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.