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

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Showing element 451 to 500 of 77072 in total

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description	Rank	Value Type	Interaction Map	Network Comparison Type	green	red	network_comparison
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1511	Measured	High confidence	Subtracted	6362.33	5926.76	435.57
	1527			Divided			1.07349
	1841		Low confidence	Subtracted	8372.5	8111.49	261.01
	1916	Rooted	High confidence	Divided	64.4831	62.679	1.02878
	1949			Subtracted			1.8041
	2003	Measured	Low confidence	Divided	8372.5	8111.49	1.03218
	2219	Rooted		Subtracted	75.0673	72.5833	2.484
	2293			Divided			1.03422
	2466	Ranked	High confidence	Subtracted	217.285	216.64	0.645
	2474			Divided			1.00298
	2595		Low confidence		196.948	200.484	1.01795
	2596			Subtracted			3.536
	3664	Squared			44725.2	46080.5	1355.3
	3788			Divided			1.0303
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1060	Measured		Subtracted	8556.58	8257.44	299.14
	1203			Divided			1.03623
	1222	Squared	High confidence	Subtracted	29299.3	26277.3	3022
	1489			Divided			1.115
	1542	Rooted	Low confidence	Subtracted	75.8817	73.251	2.6307
	1567	Measured	High confidence	Divided	6242.94	5822.25	1.07226
	1628			Subtracted			420.69
	1667	Rooted	Low confidence	Divided	75.8817	73.251	1.03591
	1991	Ranked			195.763	199.582	1.01951
	2043	Rooted	High confidence	Subtracted	63.9055	62.2342	1.6713
	2044	Ranked	Low confidence		195.763	199.582	3.819
		Rooted	High confidence	Divided	63.9055	62.2342	1.02686
	2323	Ranked		Subtracted	218.426	217.413	1.013
	2327			Divided			1.00466
	4581	Squared	Low confidence	Subtracted	46205.5	47024.3	818.8
	4609			Divided			1.01772
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	877	Measured		Subtracted	8703.92	8385.76	318.16
	1024			Divided			1.03794
	1224	Squared	High confidence	Subtracted	29163.8	26142.6	3021.2
	1481			Divided			1.11557
	1539	Measured			6207.5	5783.97	1.07322
	1578	Rooted	Low confidence	Subtracted	76.5062	73.8873	2.6189
	1622	Measured	High confidence		6207.5	5783.97	423.53
	1844	Rooted	Low confidence	Divided	76.5062	73.8873	1.03544
	1979		High confidence		63.6738	61.9542	1.02776
	2006			Subtracted			1.7196
	2321	Ranked	Low confidence	Divided	194.732	198.366	1.01866
	2394		High confidence	Subtracted	219.014	218.192	0.822
	2395			Divided			1.00377
	2407		Low confidence	Subtracted	194.732	198.366	3.634
	4819	Squared			47560.6	47959.2	398.6
	4841			Divided			1.00838
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]	453		High confidence	Subtracted	53788.1	59318.4	5530.3
	797		Low confidence		44326.9	46535.2	2208.3
	864			Divided			1.04982
	1637	Ranked	High confidence		199.408	202.358	1.01479

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.