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	Interaction Map	red	network_comparison	Gene	Network Comparison Type	Rank

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Showing element 451 to 500 of 77072 in total

Value Type  : Measured

description	Filtered	green	Interaction Map	red	network_comparison	Network Comparison Type	Rank
40s ribosomal protein s5. [swissprot;acc:p46782]	1	7645.87	Low confidence	7495.04	1.02012	Divided	4222
					150.83	Subtracted	4458
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]		6186.39	High confidence	5782.92	1.06977	Divided	1642
					403.47	Subtracted	1679
		8023.9	Low confidence	7780.28	1.03131	Divided	2244
					243.62	Subtracted	2401
40s ribosomal protein s8. [swissprot;acc:p09058]		6087.55	High confidence	5659.45	1.07564	Divided	1471
					428.1	Subtracted	1587
		8569.5	Low confidence	8525.9	1.00511	Divided	4923
					43.6	Subtracted	4917
40s ribosomal protein s9. [swissprot;acc:p46781]		3877.14	High confidence	3933.74	1.0146	Divided	2628
					56.6	Subtracted	2654
		7908.36	Low confidence	7711.01	1.02559	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		827.585	1.01302	Divided	743
					10.779	Subtracted	785
		1104.61	High confidence	1212.82	1.09796	Divided	315
					108.21	Subtracted	266
	1	5275.76		5078.5	1.03884	Divided	2402
					197.26	Subtracted	2373
		8125.51	Low confidence	7919.03	1.02607	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	High confidence	6160.06	1.07804	Divided	1402
					480.72	Subtracted	1261
		8261.9	Low confidence	8052.19	1.02604	Divided	3491
					209.71	Subtracted	3427
44050 protein. [refseq;acc:nm_178832]		8507.06		8386.63	1.01436	Divided	4703
					120.43	Subtracted	4674
		14889.2	High confidence	17385.9	1.16769	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	Low confidence	7995.61	1.04566	Divided	587
					365.11	Subtracted	598
		8570.11	High confidence	7813.48	1.09684	Divided	972
					756.63	Subtracted	576
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]		7747.63		6920.69	1.11949	Divided	691
					826.94	Subtracted	507
		8348.29	Low confidence	8139.14	1.0257	Divided	3556
					209.15	Subtracted	3436
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]		7747.63	High confidence	6920.69	1.11949	Divided	689
					826.94	Subtracted	505
		8347.85	Low confidence	8136.52	1.02597	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	High confidence	6920.67	1.11949	Divided	688
					826.93	Subtracted	509
		8396.61	Low confidence	8168.9	1.02788	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	High confidence	6920.71	1.11949	Divided	687
					826.94	Subtracted	504
		8396.61	Low confidence	8169.23	1.02783	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.