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	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1001 to 1050 of 6456 in total

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

description	Rank	Network Comparison Type	red	green	network_comparison
carboxypeptidase b precursor. [refseq;acc:nm_020361]	509	Divided	177.698	190.239	1.07057
	617	Subtracted			12.541
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	691		223.121	211.685	11.436
	717	Divided			1.05402
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	689	Subtracted			11.436
	715	Divided			1.05402
carcinoma related gene. [refseq;acc:nm_016041]	3179		0.00001	0.00001	1
		Subtracted	0	0	0
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]	1692		217.624	214.69	2.934
	1698	Divided			1.01367
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	2885		0.00001	0.00001	1
		Subtracted	0	0	0
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	141		239.991	269.238	29.247
	226	Divided			1.12187
casein kinase i alpha s-like. [refseq;acc:nm_145203]	1427	Subtracted	229.459	225.237	4.222
	1495	Divided			1.01874
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]	1428	Subtracted			4.222
	1496	Divided			1.01874
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	1679	Subtracted	227.125	224.164	2.961
	1721	Divided			1.01321
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	1663	Subtracted	227.225	224.21	3.015
	1710	Divided			1.01345
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]	2830		0.00001	0.00001	1
		Subtracted	0	0	0
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368]	2986	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]	2901	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]	885		232.473	224.372	8.101
	936	Divided			1.03611
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	810	Subtracted	240.194	230.957	9.237
	863	Divided			1.03999
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]	811	Subtracted			9.237
	864	Divided			1.03999
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210]	1165	Subtracted	233.942	228.46	5.482
	1292	Divided			1.024
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]	1834		180.409	182.459	1.01136
	1956	Subtracted			2.05
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	1667	Divided	214.898	211.898	1.01416
	1672	Subtracted			3
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]	1390		214.717	219.157	4.44
	1426	Divided			1.02068
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	1389	Subtracted			4.44
	1425	Divided			1.02068
caveolin-1. [swissprot;acc:q03135]	3099		0.00001	0.00001	1
		Subtracted	0	0	0
caveolin-3 (m-caveolin). [swissprot;acc:p56539]	2779	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
cbf1 interacting corepressor. [refseq;acc:nm_004882]	555		227.86	213.945	13.915
	572	Divided			1.06504

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.