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

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Showing element 494 to 543 of 3228 in total

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

Rank	description	red	green	network_comparison
494	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	220.172	235.98	1.0718
495	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	220.171	235.979
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	250.938	234.134	1.07177
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	251.344	234.514
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	220.161	235.95	1.07172
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	231.496	248.048	1.0715
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	224.662	240.673	1.07127
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	238.704	255.68	1.07112
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
504	oligophrenin 1. [swissprot;acc:o60890]
505	ad24 protein. [refseq;acc:nm_022451]	251.334	234.672	1.071
506	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	224.535	240.476
507	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	251.299	234.729	1.07059
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	177.698	190.24	1.07058
509	carboxypeptidase b precursor. [refseq;acc:nm_020361]		190.239	1.07057
510	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	177.699	190.24
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	250.053	233.725	1.06986
512	block of proliferation 1. [swissprot;acc:q14137]	250.794	234.433	1.06979
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	218.596	204.344	1.06975
514	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	218.613	204.382	1.06963
515	pescadillo homolog 1. [swissprot;acc:o00541]	251.297	234.941	1.06962
516	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	228.255	213.422	1.0695
517	metaxin 2. [swissprot;acc:o75431]	219.537	234.793	1.06949
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	250.858	234.563	1.06947
519	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	218.702	204.582	1.06902
520	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	214.754	229.565	1.06897
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	215.237	230.07	1.06891
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	222.893	208.523
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	215.237	230.07
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]
525	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]
526	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	250.538	234.401	1.06884
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	248.56	232.579	1.06871
528	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	222.146	237.393	1.06864
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	251.653	235.506	1.06856
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	227.483	212.994	1.06803
531	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	223.356	209.149	1.06793
532	zinc finger-like protein 9. [refseq;acc:nm_033414]	250.942	235.004	1.06782
533	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	236.662	252.708	1.0678
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	242.531	227.136	1.06778
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	229.803	215.301	1.06736
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	237.627	253.604	1.06724
539	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	236.964	252.86	1.06708
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	222.156	208.201	1.06703
541	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
542	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
543	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]

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.