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	Interaction Map	Filtered	green	Network Comparison Type	red	network_comparison

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Showing element 51 to 100 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

description	Rank	green	Network Comparison Type	red	network_comparison
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]	1637	199.408	Divided	202.358	1.01479
	1682		Subtracted		2.95
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	2478	216.801	Divided	216.177	1.00289
	2486		Subtracted		0.624
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	2355	219.434		218.555	0.879
	2368		Divided		1.00402
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	2256	218.627	Subtracted	217.419	1.208
	2269		Divided		1.00556
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	2353	218.475	Subtracted	217.589	0.886
	2367		Divided		1.00407
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	2300	218.311	Subtracted	217.241	1.07
	2316		Divided		1.00493
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	2324	218.116	Subtracted	217.112	1.004
	2329		Divided		1.00462
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	2169	208.808	Subtracted	210.209	1.401
	2175		Divided		1.00671
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	2423	218.376	Subtracted	217.645	0.731
	2440		Divided		1.00336
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]	1377	225.468	Subtracted	220.987	4.481
	1432		Divided		1.02028
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	2419	216.556	Subtracted	215.807	0.749
	2432		Divided		1.00347
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	2350	218.162	Subtracted	217.232	0.93
	2355		Divided		1.00428
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	2519	216.341	Subtracted	215.835	0.506
	2525		Divided		1.00234
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	2620	215.91		215.615	1.00137
	2627		Subtracted		0.295
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	2127	219.366		217.871	1.495
	2150		Divided		1.00686
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	798	221.785	Subtracted	212.386	9.399
	810		Divided		1.04425
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	235	268.195	Subtracted	243.944	24.251
	325		Divided		1.09941
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	2151	225.854	Subtracted	224.411	1.443
	2212		Divided		1.00643
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	23	44		58	1.31818
	533		Subtracted		14
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	1656	214.826		217.925	3.099
	1659		Divided		1.01443
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2673	215.108	Subtracted	214.893	0.215
	2675		Divided		1.001
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	340	260.544	Subtracted	239.75	20.794
	407		Divided		1.08673
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	3147	0	Subtracted	0	0
		0.00001	Divided	0.00001	1
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	2756	0	Subtracted	0	0
		0.00001	Divided	0.00001	1
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]	2802	0	Subtracted	0	0
		0.00001	Divided	0.00001	1

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.