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	Filtered	Interaction Map	Network Comparison Type	red	network_comparison	green

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Showing element 101 to 150 of 19268 in total

Value Type  : Measured

description	Rank	Filtered	Interaction Map	Network Comparison Type	red	network_comparison	green
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	19	0	High confidence	Divided	305.45	11.6763	26.1599
		1	Low confidence		3032.56	1.29112	3915.4
	107			Subtracted		882.84
	115	0	High confidence		305.45	279.29	26.1599
	171		Low confidence	Divided	222.779	1.22585	181.734
	635			Subtracted		41.045
	3079	1	High confidence	Divided	0.00001	1	0.00001
				Subtracted	0	0	0
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	1491				5938.56	438.2	6376.76
	1521			Divided		1.07379
	1677		Low confidence	Subtracted	8156.56	266.11	8422.67
	1881			Divided		1.03263
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1511		High confidence	Subtracted	5926.76	435.57	6362.33
	1527			Divided		1.07349
	1841		Low confidence	Subtracted	8111.49	261.01	8372.5
	2003			Divided		1.03218
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1060			Subtracted	8257.44	299.14	8556.58
	1203			Divided		1.03623
	1567		High confidence		5822.25	1.07226	6242.94
	1628			Subtracted		420.69
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	877		Low confidence		8385.76	318.16	8703.92
	1024			Divided		1.03794
	1539		High confidence		5783.97	1.07322	6207.5
	1622			Subtracted		423.53
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	2602				9150.44	83.65	9234.09
	2651			Divided		1.00914
	2944		Low confidence	Subtracted	8088.94	225.57	8314.51
	3044			Divided		1.02789
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577		High confidence		5923.66	1.07181	6349.04
	1599			Subtracted		425.38
	2526		Low confidence		8088.12	238.39	8326.51
	2711			Divided		1.02947
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1862		High confidence	Subtracted	5826	369.48	6195.48
	1883			Divided		1.06342
	2447		Low confidence		7825.14	1.03046	8063.51
	2527			Subtracted		238.37
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	380	0	High confidence		2683.61	40.82	2642.79
	451			Divided		1.01545
	762		Low confidence	Subtracted	1593.68	16.2	1609.88
	771			Divided		1.01017
	1609	1	High confidence		5826.74	1.07134	6242.44
	1646			Subtracted		415.7
	1884		Low confidence		8137.96	259.6	8397.56
	2056			Divided		1.0319
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	744			Subtracted	8393.58	334.41	8727.99
	889			Divided		1.03984
	1592		High confidence		5853.1	1.07153	6271.79
	1634			Subtracted		418.69
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	434	0			2281.12	17.27	2263.85
	474			Divided		1.00763

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.