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	Filtered	Value Type	Network Comparison Type	green	Interaction Map	red	network_comparison

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description	Rank	Value Type	Network Comparison Type	green	Interaction Map	red	network_comparison
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	1511	Measured	Subtracted	6362.33	High confidence	5926.76	435.57
	1527		Divided				1.07349
	1841		Subtracted	8372.5	Low confidence	8111.49	261.01
	1916	Rooted	Divided	64.4831	High confidence	62.679	1.02878
	1949		Subtracted				1.8041
	2003	Measured	Divided	8372.5	Low confidence	8111.49	1.03218
	2219	Rooted	Subtracted	75.0673		72.5833	2.484
	2293		Divided				1.03422
	2466	Ranked	Subtracted	217.285	High confidence	216.64	0.645
	2474		Divided				1.00298
	2595			196.948	Low confidence	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	Subtracted	29299.3	High confidence	26277.3	3022
	1489		Divided				1.115
	1542	Rooted	Subtracted	75.8817	Low confidence	73.251	2.6307
	1567	Measured	Divided	6242.94	High confidence	5822.25	1.07226
	1628		Subtracted				420.69
	1667	Rooted	Divided	75.8817	Low confidence	73.251	1.03591
	1991	Ranked		195.763		199.582	1.01951
	2043	Rooted	Subtracted	63.9055	High confidence	62.2342	1.6713
	2044	Ranked		195.763	Low confidence	199.582	3.819
		Rooted	Divided	63.9055	High confidence	62.2342	1.02686
	2323	Ranked	Subtracted	218.426		217.413	1.013
	2327		Divided				1.00466
	4581	Squared	Subtracted	46205.5	Low confidence	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	Subtracted	29163.8	High confidence	26142.6	3021.2
	1481		Divided				1.11557
	1539	Measured		6207.5		5783.97	1.07322
	1578	Rooted	Subtracted	76.5062	Low confidence	73.8873	2.6189
	1622	Measured		6207.5	High confidence	5783.97	423.53
	1844	Rooted	Divided	76.5062	Low confidence	73.8873	1.03544
	1979			63.6738	High confidence	61.9542	1.02776
	2006		Subtracted				1.7196
	2321	Ranked	Divided	194.732	Low confidence	198.366	1.01866
	2394		Subtracted	219.014	High confidence	218.192	0.822
	2395		Divided				1.00377
	2407		Subtracted	194.732	Low confidence	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		Subtracted	53788.1	High confidence	59318.4	5530.3
	797			44326.9	Low confidence	46535.2	2208.3
	864		Divided				1.04982
	1637	Ranked		199.408	High confidence	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.