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	Value Type	Gene	description	Rank	Filtered	Interaction Map	network_comparison	red	green

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Showing element 768 to 817 of 3228 in total

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

description	Rank	network_comparison	red	green
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]	1039	1.03137	207.719	214.236
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]	1462	1.0196	205.817	209.851
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]	2392	1.00388	214.966	215.799
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	1009	1.03288	229.116	221.823
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	2213	1.00642	210.127	211.475
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740]	2288	1.00533	216.607	215.458
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518]	2286	1.00535	216.608	215.456
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	2276	1.00541	216.613	215.448
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512]	2289	1.00531	216.605	215.46
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326]	2271	1.00551	216.622	215.436
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	1516	1.01793	213.267	209.511
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	395	1.08948	218.827	238.407
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	1515	1.01793	213.267	209.511
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	394	1.08948	218.827	238.407
diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	868	1.03975	233.298	242.571
diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]	1202	1.02537	227.274	233.041
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]	701	1.05413	220.438	209.118
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	708
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]	706
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]	710
disrupter of silencing 10. [refseq;acc:nm_020368]	1905	1.01034	191.411	193.39
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	724	1.05274	244.842	232.577
dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]	2060	1.00834	218.79	216.981
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	776	1.04854	225.996	215.535
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]	1287	1.02414	218.368	213.22
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	576	1.0648	235.18	250.419
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	2621	1.00135	224.891	225.195
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2408	1.00362	194.407	193.706
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	3025	1	0.00001	0.00001
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	700	1.05413	220.438	209.118
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	1125	1.02748	204.404	210.022
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	222	1.125	112	126
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	177	1.1663	229.406	196.695
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	1881	1.01074	210.592	208.355
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	1329	1.02275	218.509	213.648
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	1326
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	339	1.0983	243.583	267.527
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	1029	1.03168	222.364	215.535
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	906	1.03838	230.764	239.62
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	905	1.03841	230.768	239.632
dna excision repair protein ercc-1. [swissprot;acc:p07992]	3216	1	0.00001	0.00001
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	2515	1.00234	215.835	216.341
dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	2517
dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858]	3103	1	0.00001	0.00001
dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]	2808
dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5]	2796
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	1878	1.01075	212.186	214.467
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	1749	1.01264	206.058	203.485
dna mismatch repair protein msh2. [swissprot;acc:p43246]	3151	1	0.00001	0.00001
dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]	3045

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.