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

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Showing element 501 to 550 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Network Comparison Type	Rank	red	Value Type	green	network_comparison
40s ribosomal protein s13. [swissprot;acc:q02546]	Subtracted	936	21976	Squared	25607.9	3631.9
		1677	5414.98	Measured	5818.7	403.72
		1695	220.899	Ranked	223.813	2.914
		2361	60.5137	Rooted	61.6019	1.0882
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	Divided	386	242.238	Ranked	264.11	1.09029
		530	50.6537	Rooted	46.6413	1.08603
		1823	13145.4	Squared	14424.1	1.09727
		2436	3708.67	Measured	3584.47	1.03465
	Subtracted	323	242.238	Ranked	264.11	21.872
		824	50.6537	Rooted	46.6413	4.0124
		2418	13145.4	Squared	14424.1	1278.7
		2520	3708.67	Measured	3584.47	124.2
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Divided	304	242.339	Ranked	266.986	1.1017
		376	50.2554	Rooted	45.5688	1.10285
		1989	12388.6	Squared	13523.5	1.09161
		2067	3602.75	Measured	3411.18	1.05616
	Subtracted	219	242.339	Ranked	266.986	24.647
		651	50.2554	Rooted	45.5688	4.6866
		2391	3602.75	Measured	3411.18	191.57
		2497	12388.6	Squared	13523.5	1134.9
40s ribosomal protein s15a. [swissprot;acc:p39027]	Divided	292	241.411	Ranked	266.414	1.10357
		366	50.5463	Rooted	45.7763	1.1042
		2008	3637.47	Measured	3435.61	1.05876
		2015	12467.2	Squared	13600.6	1.09091
	Subtracted	206	241.411	Ranked	266.414	25.003
		615	50.5463	Rooted	45.7763	4.77
		2368	3637.47	Measured	3435.61	201.86
		2502	12467.2	Squared	13600.6	1133.4
40s ribosomal protein s16. [swissprot;acc:p17008]	Divided	391	241.828	Ranked	263.62	1.09011
		534	50.8036	Rooted	46.8198	1.08509
		1784	13244.1	Squared	14564.4	1.09969
		2448	3730.53	Measured	3611.05	1.03309
	Subtracted	326	241.828	Ranked	263.62	21.792
		830	50.8036	Rooted	46.8198	3.9838
		2407	13244.1	Squared	14564.4	1320.3
		2528	3730.53	Measured	3611.05	119.48
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Divided	387	242.238	Ranked	264.11	1.09029
		531	50.6537	Rooted	46.6413	1.08603
		1824	13145.4	Squared	14424.1	1.09727
		2437	3708.67	Measured	3584.47	1.03465
	Subtracted	324	242.238	Ranked	264.11	21.872
		825	50.6537	Rooted	46.6413	4.0124
		2419	13145.4	Squared	14424.1	1278.7
		2521	3708.67	Measured	3584.47	124.2
40s ribosomal protein s19. [swissprot;acc:p39019]	Divided	771	55.6817	Rooted	59.3786	1.06639
		807	4708.61	Measured	5226.71	1.11003
		861	234.025	Ranked	224.958	1.04031
		1129	18854.4	Squared	21540.4	1.14246
	Subtracted	820	234.025	Ranked	224.958	9.067
		907	55.6817	Rooted	59.3786	3.6969

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.