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 951 to 1000 of 3228 in total

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

description	Rank	red	green	network_comparison
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
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	1839	221.525	224.001	1.01118
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	1865	221.639	224.046	1.01086
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]	904	246.354	237.223	1.03849
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	1565	221.128	224.767	1.01646
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	746	250.465	238.38	1.0507
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	903	246.354	237.223	1.03849
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]	1571	221.128	224.767	1.01646
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]	1931	219.753	217.574	1.01001
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	1405	245.532	240.483	1.021
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	822	243.067	232.805	1.04408
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	252	237.292	212.457	1.11689
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	246	237.312	212.363	1.11748
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	649	233.725	220.751	1.05877
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	268	271.016	244.167	1.10996
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	2102	208.727	210.263	1.00736
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	545	248.866	233.287	1.06678
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	573	227.86	213.945	1.06504
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	2092	211.992	210.369	1.00772
exocyst complex component exo70. [swissprot;acc:q9upt5]	2781	0.00001	0.00001	1
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	721	214.765	203.8	1.0538
exocyst complex component sec15a. [swissprot;acc:q8tag9]	750	222.138	211.503	1.05028
exocyst complex component sec15b. [swissprot;acc:q9y2d4]	749	221.968	211.326	1.05036
exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	2487	218.093	218.72	1.00287
exocyst complex component sec5. [swissprot;acc:q96kp1]	986	116.771	120.707	1.03371
exocyst complex component sec6. [swissprot;acc:o60645]	981	207.186	200.398	1.03387
exocyst complex component sec8. [swissprot;acc:q96a65]	869	217.762	209.449	1.03969
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	1344	216.772	221.594	1.02224
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	523	215.237	230.07	1.06891
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	524
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	521
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	525
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	1497	224.476	220.363	1.01866
eyes absent homolog 1. [swissprot;acc:q99502]	1396	218.463	213.872	1.02147

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.