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	green	red	network_comparison

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Showing element 501 to 550 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	green	red	network_comparison
carboxypeptidase b precursor. [refseq;acc:nm_020361]	239	6265.8	7711.38	1.23071
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	719	7364.55	6593.17	1.117
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]	717
carcinoma related gene. [refseq;acc:nm_016041]	3179	0.00001	0.00001	1
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]	1093	6316.61	5791.05	1.09075
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	2885	0.00001	0.00001	1
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	2220	3755.33	3936.2	1.04816
casein kinase i alpha s-like. [refseq;acc:nm_145203]	953	5382.5	4906.33	1.09705
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]	954
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	1035	5530.23	5054.73	1.09407
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	1030	5523.85	5048.33	1.09419
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]	2830	0.00001	0.00001	1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368]	2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]	2901
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]	1245	5243.23	4835.55	1.08431
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	851	4755.03	4307.12	1.10399
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]	852
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210]	948	5084.24	4633.48	1.09728
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]	616	9948.93	11222.2	1.12798
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	914	7161	6513.45	1.09942
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]	2238	6181.21	5902.27	1.04726
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	2237		5902.26
caveolin-1. [swissprot;acc:q03135]	3099	0.00001	0.00001	1
caveolin-3 (m-caveolin). [swissprot;acc:p56539]	2779
cbf1 interacting corepressor. [refseq;acc:nm_004882]	1651	6358.1	5944.24	1.06962
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	507	7858.38	6875.08	1.14302
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	257	7858.12	6417.31	1.22452
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	137	4763.34	3620.77	1.31556
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	369	4194.95	3583.56	1.17061
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516]	3163	0.00001	0.00001	1
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]	2289	6048.94	5783.76	1.04585
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571]	2958	0.00001	0.00001	1
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	3226
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9]	2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	1445	5510.45	5117.85	1.07671
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	2753	4521.87	4521.42	1.0001
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	2755
cda11 protein. [refseq;acc:nm_032026]	1174	6387.23	5874.11	1.08735
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]	1995	6538.73	6174.74	1.05895
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	1611	5132.35	5497.73	1.07119
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	419	6350.19	5493.1	1.15603
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]	3209	0.00001	0.00001	1
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]	981	7296.51	6654.42	1.09649
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	1660	7950.61	7433.73	1.06953
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	363	10876.4	12780.7	1.17509
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	2387	7940.87	8265.85	1.04092
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	361	10880.5	12787.6	1.17528
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	359	10887.2	12798.9	1.17559
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535]	2850	0.00001	0.00001	1
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	2990

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.