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	Value Type	Interaction Map	Filtered	Network Comparison Type	red	network_comparison	green

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Showing element 551 to 600 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

description	Rank	Value Type	Filtered	red	network_comparison	green
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	262	Squared	0	2463.89	1.25915	3102.4
	269	Measured		1217.92	1.12309	1367.83
	357	Ranked	1	243.12	1.09683	266.661
	444	Rooted		50.1636	1.09701	45.7275
	1895	Squared		12581.2	1.09413	13765.5
	2233	Measured		3614.08	1.04754	3450.07
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	259	Squared	0	3438.01	1.26235	4339.96
	322	Measured		1621.1	1.09249	1771.04
	355	Rooted		27.6061	1.04709	28.9062
	356	Ranked	1	243.24	1.09684	266.796
	397		0	10006.9	1.03414	9676.53
	443	Rooted	1	50.1766	1.09707	45.7369
	1906	Squared		12688.5	1.09397	13880.9
	2255	Measured		3624.59	1.04655	3463.37
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	373	Ranked		242.37	1.09442	265.255
	509	Rooted		50.2583	1.09122	46.057
	1743	Squared		12299.6	1.10078	13539.1
	2417	Measured		3598.55	1.03775	3467.65
60s ribosomal protein l11. [swissprot;acc:p39026]	283	Ranked		241.828	1.10552	267.346
	336	Rooted		50.3167	1.10814	45.4063
	1834	Measured		3593.24	1.06437	3375.93
	2108	Squared		12200.6	1.08823	13277
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	265		0	3687.69	1.25845	4640.77
	330	Measured		1658.23	1.08882	1805.52
	338	Ranked	1	243.583	1.0983	267.528
	362	Rooted	0	27.5242	1.04491	28.7604
	396	Ranked		10194.8	1.03436	9856.12
	407	Rooted	1	49.9856	1.09996	45.4431
	1933	Squared		12442.9	1.09354	13606.8
	2186	Measured		3586.3	1.05035	3414.4
60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	369	Ranked		242.159	1.09475	265.104
	489	Rooted		50.5505	1.09228	46.2797
	1878	Squared		12933	1.09484	14159.6
	2372	Measured		3677.53	1.04278	3526.65
60s ribosomal protein l12. [swissprot;acc:p30050]	264	Squared	0	3686.65	1.25845	4639.46
	328	Measured		1657.78	1.08884	1805.05
	337	Ranked	1	243.583	1.0983	267.527
	360	Rooted	0	27.5183	1.04493	28.7547
	394	Ranked		10196.9	1.0344	9857.79
	406	Rooted	1	49.9858	1.09996	45.4433
	1931	Squared		12442.9	1.09355	13606.9
	2185	Measured		3586.32	1.05035	3414.42
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	390	Ranked		241.828	1.09011	263.62
	533	Rooted		50.8036	1.08509	46.8198
	1783	Squared		13244.1	1.09969	14564.4
	2447	Measured		3730.53	1.03309	3611.05
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	392	Ranked		241.83	1.09008	263.615
	535	Rooted		50.8041	1.08505	46.8218
	1782	Squared		13245.8	1.09971	14566.6
	2449	Measured		3730.74	1.03303	3611.45

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.