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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 3228 in total

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

Rank	green	description	red	network_comparison
501	255.68	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	238.704	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	234.672	ad24 protein. [refseq;acc:nm_022451]	251.334	1.071
506	240.476	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	224.535
507	234.729	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	251.299	1.07059
508	190.24	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	177.698	1.07058
509	190.239	carboxypeptidase b precursor. [refseq;acc:nm_020361]		1.07057
510	190.24	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
511	233.725	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	250.053	1.06986
512	234.433	block of proliferation 1. [swissprot;acc:q14137]	250.794	1.06979
513	204.344	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	218.596	1.06975
514	204.382	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	218.613	1.06963
515	234.941	pescadillo homolog 1. [swissprot;acc:o00541]	251.297	1.06962
516	213.422	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	228.255	1.0695
517	234.793	metaxin 2. [swissprot;acc:o75431]	219.537	1.06949
518	234.563	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	250.858	1.06947
519	204.582	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	218.702	1.06902
520	229.565	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	214.754	1.06897
521	230.07	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	215.237	1.06891
522	208.523	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	222.893
523	230.07	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	215.237
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	234.401	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	250.538	1.06884
527	232.579	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	248.56	1.06871
528	237.393	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	222.146	1.06864
529	235.506	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	251.653	1.06856
530	212.994	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	227.483	1.06803
531	209.149	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	223.356	1.06793
532	235.004	zinc finger-like protein 9. [refseq;acc:nm_033414]	250.942	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	252.708	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	1.0678
536	227.136	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	242.531	1.06778
537	215.301	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	229.803	1.06736
538	253.604	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	237.627	1.06724
539	252.86	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	236.964	1.06708
540	208.201	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	222.156	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]
544		inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
545	233.287	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	248.866	1.06678
546	194.262	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	207.222	1.06671
547	194.346	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	207.26	1.06645
548		tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
549		proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
550		tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]

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.