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	network_comparison	green	Filtered	Interaction Map	red

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Showing element 968 to 1017 of 3228 in total

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

description	Rank	network_comparison	green	red
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	1839	1.01118	224.001	221.525
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	1865	1.01086	224.046	221.639
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]	904	1.03849	237.223	246.354
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	1565	1.01646	224.767	221.128
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	1.0507	238.38	250.465
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	903	1.03849	237.223	246.354
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]	1571	1.01646	224.767	221.128
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]	1931	1.01001	217.574	219.753
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	1405	1.021	240.483	245.532
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	822	1.04408	232.805	243.067
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	252	1.11689	212.457	237.292
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	246	1.11748	212.363	237.312
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	649	1.05877	220.751	233.725
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	268	1.10996	244.167	271.016
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	2102	1.00736	210.263	208.727
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	545	1.06678	233.287	248.866
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	573	1.06504	213.945	227.86
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	2092	1.00772	210.369	211.992
exocyst complex component exo70. [swissprot;acc:q9upt5]	2781	1	0.00001	0.00001
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	721	1.0538	203.8	214.765
exocyst complex component sec15a. [swissprot;acc:q8tag9]	750	1.05028	211.503	222.138
exocyst complex component sec15b. [swissprot;acc:q9y2d4]	749	1.05036	211.326	221.968
exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	2487	1.00287	218.72	218.093
exocyst complex component sec5. [swissprot;acc:q96kp1]	986	1.03371	120.707	116.771
exocyst complex component sec6. [swissprot;acc:o60645]	981	1.03387	200.398	207.186
exocyst complex component sec8. [swissprot;acc:q96a65]	869	1.03969	209.449	217.762
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	1344	1.02224	221.594	216.772
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	523	1.06891	230.07	215.237
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	1.01866	220.363	224.476
eyes absent homolog 1. [swissprot;acc:q99502]	1396	1.02147	213.872	218.463
eyes absent homolog 2. [swissprot;acc:o00167]	1399	1.02137	213.848	218.417
eyes absent homolog 3. [swissprot;acc:q99504]	1376	1.02163	213.91	218.537
eyes absent homolog 4. [swissprot;acc:o95677]	1398	1.02144	213.864	218.449
ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]	3228	1	0.00001	0.00001
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	1824	1.0115	212.281	214.722
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	1831	1.01139	212.328	214.746
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	2032	1.00872	213.46	215.322
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]	2033
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	209	1.13261	252.234	285.684
fad synthetase. [refseq;acc:nm_025207]	270	1.10763	267.352	241.373
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	2656	1.00109	216.943	217.179
farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]	2462	1.00308	235.088	235.812
fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	2068	1.0082	222.61	220.8
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	1442	1.02015	229.573	225.039
fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]	1441
fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]	1439
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]	1536	1.01732	232.376	228.419

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.