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

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description	Value Type	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared	426	Subtracted	3.3189	High confidence	22.8932	26.2121
		560	Divided	1.08516	Low confidence	42399.1	46009.8
	Rooted	338	Subtracted	2.3504		30.3368	27.9864
		384	Divided	1.03648	High confidence	12.8903	13.3606
		406		1.08398	Low confidence	30.3368	27.9864
		436	Subtracted	0.4703	High confidence	12.8903	13.3606
60s ribosomal protein l15. [swissprot;acc:p39030]	Measured	272	Divided	1.12261		753.793	846.216
		284	Subtracted	92.423
		599	Divided	1.03681	Low confidence	1035.81	1073.94
		642	Subtracted	38.13
	Ranked	167		1457.9	High confidence	13203.1	11745.2
		188	Divided	1.12413
		296	Subtracted	888.8	Low confidence	12972.6	12083.8
		447	Divided	1.07355
	Squared	300	Subtracted	76.23	High confidence	1286.61	1362.84
		410	Divided	1.05925
		577	Subtracted	122.05	Low confidence	4629.2	4507.15
		721	Divided	1.02708
	Rooted	186		1.14233	High confidence	17.0546	19.482
		233	Subtracted	2.4274
		413	Divided	1.07878	Low confidence	18.2577	19.6961
		476	Subtracted	1.4384
60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Measured	138		242.55	High confidence	1906.28	1663.73
		228		245.05	Low confidence	2987.56	2742.51
		232	Divided	1.14579	High confidence	1906.28	1663.73
		422		1.08935	Low confidence	2987.56	2742.51
	Ranked	277		1.08245	High confidence	10251.6	11096.8
		281	Subtracted	845.2
		605		371.5	Low confidence	10757.5	11129
		607	Divided	1.03453
	Squared	97	Subtracted	2828.5		21937.1	19108.6
		118		1037.64	High confidence	5159.2	4121.56
		269	Divided	1.25176
		334		1.14802	Low confidence	21937.1	19108.6
	Rooted	210	Subtracted	2.6917	High confidence	28.761	26.0693
		262	Divided	1.10325
		399	Subtracted	1.7624	Low confidence	31.1643	29.4019
		482	Divided	1.05994
60s ribosomal protein l18a. [swissprot;acc:q02543]	Measured	264	Subtracted	212.36		3920.97	3708.61
		313		83.99	High confidence	2604.71	2688.7
		419	Divided	1.03225
		516		1.05726	Low confidence	3920.97	3708.61
	Ranked	90	Subtracted	2301.6	High confidence	10437.1	12738.7
		102	Divided	1.22052
		617		1.03062	Low confidence	10063.9	10372.1
		629	Subtracted	308.2
	Squared	49		4855.6		26833.6	21978
		261	Divided	1.22093
		302	Subtracted	74.83	High confidence	9385.52	9310.69
		475	Divided	1.00804

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.