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

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Showing element 451 to 500 of 77072 in total

Value Type  : Measured

description	green	Filtered	Interaction Map	network_comparison	red	Rank	Network Comparison Type
40s ribosomal protein s5. [swissprot;acc:p46782]	7645.87	1	Low confidence	1.02012	7495.04	4222	Divided
				150.83		4458	Subtracted
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	6186.39		High confidence	1.06977	5782.92	1642	Divided
				403.47		1679	Subtracted
	8023.9		Low confidence	1.03131	7780.28	2244	Divided
				243.62		2401	Subtracted
40s ribosomal protein s8. [swissprot;acc:p09058]	6087.55		High confidence	1.07564	5659.45	1471	Divided
				428.1		1587	Subtracted
	8569.5		Low confidence	1.00511	8525.9	4923	Divided
				43.6		4917	Subtracted
40s ribosomal protein s9. [swissprot;acc:p46781]	3877.14		High confidence	1.0146	3933.74	2628	Divided
				56.6		2654	Subtracted
	7908.36		Low confidence	1.02559	7711.01	3586	Divided
				197.35		3684	Subtracted
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	838.364	0		1.01302	827.585	743	Divided
				10.779		785	Subtracted
	1104.61		High confidence	1.09796	1212.82	315	Divided
				108.21		266	Subtracted
	5275.76	1		1.03884	5078.5	2402	Divided
				197.26		2373	Subtracted
	8125.51		Low confidence	1.02607	7919.03	3484	Divided
				206.48		3486	Subtracted
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	6640.78		High confidence	1.07804	6160.06	1402	Divided
				480.72		1261	Subtracted
	8261.9		Low confidence	1.02604	8052.19	3491	Divided
				209.71		3427	Subtracted
44050 protein. [refseq;acc:nm_178832]	8507.06			1.01436	8386.63	4703	Divided
				120.43		4674	Subtracted
	14889.2		High confidence	1.16769	17385.9	376	Divided
				2496.7		109	Subtracted
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	8360.72		Low confidence	1.04566	7995.61	587	Divided
				365.11		598	Subtracted
	8570.11		High confidence	1.09684	7813.48	972	Divided
				756.63		576	Subtracted
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	7747.63			1.11949	6920.69	691	Divided
				826.94		507	Subtracted
	8348.29		Low confidence	1.0257	8139.14	3556	Divided
				209.15		3436	Subtracted
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	7747.63		High confidence	1.11949	6920.69	689	Divided
				826.94		505	Subtracted
	8347.85		Low confidence	1.02597	8136.52	3509	Divided
				211.33		3382	Subtracted
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	7747.6		High confidence	1.11949	6920.67	688	Divided
				826.93		509	Subtracted
	8396.61		Low confidence	1.02788	8168.9	3045	Divided
				227.71		2883	Subtracted
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	7747.65		High confidence	1.11949	6920.71	687	Divided
				826.94		504	Subtracted
	8396.61		Low confidence	1.02783	8169.23	3059	Divided
				227.38		2897	Subtracted

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.