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

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Showing element 918 to 967 of 3228 in total

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

description	Rank	red	green	network_comparison
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	1792	217.766	215.199	1.01193
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	2441	180.137	180.732	1.0033
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	2353	182.232	183.027	1.00436
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]	2016	199.092	197.301	1.00908
elks protein. [refseq;acc:nm_015064]	1061	218.162	211.648	1.03078
ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456]	2921	0.00001	0.00001	1
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	2433	217.366	218.117	1.00346
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]	2436
elongation factor 2 (ef-2). [swissprot;acc:p13639]	2557	222.658	223.047	1.00175
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	3027	0.00001	0.00001	1
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	886	227.596	219.018	1.03917
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]	1802	217.011	214.481	1.0118
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	1322	159.86	156.275	1.02294
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	432	212.547	229.411	1.07934
endosome-associated fyve-domain protein. [refseq;acc:nm_014733]	3200	0.00001	0.00001	1
endothelial-derived gene 1. [refseq;acc:nm_025205]	1918	202.211	200.18	1.01015
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	286	224.633	203.251	1.1052
enhancer of rudimentary homolog. [swissprot;acc:q14259]	2676	214.893	215.108	1.001
enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800]	3090	0.00001	0.00001	1
enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910]	3098
enigma protein; lim domain protein. [refseq;acc:nm_005451]	1929	219.753	217.574	1.01001
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	1403	184.656	180.823	1.0212
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	577	224.606	210.944	1.06477
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	1612	221.426	224.902	1.0157
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929]	1153	221.93	216.146	1.02676
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204]	1152	221.939	216.143	1.02682
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772]	1158	221.877	216.167	1.02641
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]	2005	225.019	222.971	1.00919
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	1339	205.204	200.71	1.02239
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	320	241.892	265.96	1.0995
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	2446	182.272	181.683	1.00324
epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	2430	217.873	218.644	1.00354
epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]	2550	217.587	217.988	1.00184
epsin 3. [refseq;acc:nm_017957]	2297	218.153	219.284	1.00518
ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257]	3177	0.00001	0.00001	1
ero1-like. [refseq;acc:nm_014584]	911	217.168	209.207	1.03805
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]	1566	221.128	224.767	1.01646
erythroid differentiation-related factor 1. [refseq;acc:nm_015608]	3095	0.00001	0.00001	1
espin. [refseq;acc:nm_031475]	1257	219.354	224.7	1.02437
esterase d (ec 3.1.1.1). [swissprot;acc:p10768]	2429	192.871	193.555	1.00355
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	1050	211.449	217.998	1.03097
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659]	1768	185.276	187.534	1.01219
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	1042	186.799	181.127	1.03132
ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]	2378	212.724	213.574	1.004
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9]	2377
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	1758	233.45	230.595	1.01238
eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765]	2868	0.00001	0.00001	1
eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240]	2888
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	772	210.946	221.225	1.04873
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]	1341	226.433	231.491	1.02234

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.