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	Filtered	green	network_comparison	red	Interaction Map	Gene	Network Comparison Type	Rank

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Showing element 451 to 500 of 77072 in total

Value Type  : Measured

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

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.