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

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Showing element 551 to 600 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	green	Value Type	Interaction Map	red	network_comparison
40s ribosomal protein s11. [swissprot;acc:p04643]	1873	3402.09	Measured	High confidence	3618.46	1.0636
	1939	39527.9	Squared	Low confidence	41135.5	1.04067
	2016	13514		High confidence	12389	1.09081
	3606	210.891	Ranked	Low confidence	207.913	1.01432
	4707	7472.14	Measured		7369.62	1.01391
	4898	69.4847	Rooted		68.7371	1.01088
40s ribosomal protein s12. [swissprot;acc:p25398]	3133	42497.6	Squared		43974.9	1.03476
	3276	7995.94	Measured		7785.76	1.027
	3859	72.9222	Rooted		70.9166	1.02828
	4261	201.631	Ranked		203.546	1.0095
40s ribosomal protein s13. [swissprot;acc:q02546]	776	25607.9	Squared	High confidence	21976	1.16527
	1498	5818.7	Measured		5414.98	1.07456
	1722	223.813	Ranked		220.899	1.01319
	2348	61.6019	Rooted		60.5137	1.01798
	2851	8262.44	Measured	Low confidence	8031.31	1.02878
	3405	74.2382	Rooted		72.0347	1.03059
	3619	44427.7	Squared		45834.3	1.03166
	3777	199.227	Ranked		201.886	1.01335
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	386	264.11		High confidence	242.238	1.09029
	530	46.6413	Rooted		50.6537	1.08603
	1823	14424.1	Squared		13145.4	1.09727
	2030	40034.4		Low confidence	41640.7	1.04012
	2436	3584.47	Measured	High confidence	3708.67	1.03465
	4334	7571.79		Low confidence	7425.75	1.01967
	4717	209.433	Ranked		208.268	1.00559
	4747	70.0583	Rooted		68.8727	1.01721
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	304	266.986	Ranked	High confidence	242.339	1.1017
	376	45.5688	Rooted		50.2554	1.10285
	1989	13523.5	Squared		12388.6	1.09161
	2067	3411.18	Measured		3602.75	1.05616
	2567	40220.1	Squared	Low confidence	41752.3	1.0381
	4250	209.342	Ranked		207.351	1.0096
	4587	7576.71	Measured		7449.17	1.01712
	4822	70.1036	Rooted		69.1027	1.01448
40s ribosomal protein s15a. [swissprot;acc:p39027]	292	266.414	Ranked	High confidence	241.411	1.10357
	366	45.7763	Rooted		50.5463	1.1042
	1303	40292.9	Squared	Low confidence	42102.8	1.04492
	2008	3435.61	Measured	High confidence	3637.47	1.05876
	2015	13600.6	Squared		12467.2	1.09091
	3989	209.395	Ranked	Low confidence	206.934	1.01189
	4697	7588.58	Measured		7480.2	1.01449
	4864	70.1434	Rooted		69.2629	1.01271
40s ribosomal protein s16. [swissprot;acc:p17008]	391	263.62	Ranked	High confidence	241.828	1.09011
	534	46.8198	Rooted		50.8036	1.08509
	1784	14564.4	Squared		13244.1	1.09969
	2448	3611.05	Measured		3730.53	1.03309
	2770	40856.6	Squared	Low confidence	42362	1.03685
	4134	7653.76	Measured		7496.15	1.02103
	4676	70.3804	Rooted		69.0873	1.01872
	4832	209.034	Ranked		208.276	1.00364

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.