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	Rank	description	Interaction Map	green	network_comparison	red	Filtered

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Showing element 513 to 562 of 3228 in total

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

Rank	description	green	network_comparison	red
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	204.344	1.06975	218.596
514	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	204.382	1.06963	218.613
515	pescadillo homolog 1. [swissprot;acc:o00541]	234.941	1.06962	251.297
516	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	213.422	1.0695	228.255
517	metaxin 2. [swissprot;acc:o75431]	234.793	1.06949	219.537
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	234.563	1.06947	250.858
519	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	204.582	1.06902	218.702
520	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	229.565	1.06897	214.754
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	230.07	1.06891	215.237
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	208.523		222.893
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	230.07		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	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	234.401	1.06884	250.538
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	232.579	1.06871	248.56
528	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	237.393	1.06864	222.146
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	235.506	1.06856	251.653
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	212.994	1.06803	227.483
531	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	209.149	1.06793	223.356
532	zinc finger-like protein 9. [refseq;acc:nm_033414]	235.004	1.06782	250.942
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]	252.708	1.0678	236.662
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	227.136	1.06778	242.531
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	215.301	1.06736	229.803
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	253.604	1.06724	237.627
539	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	252.86	1.06708	236.964
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	208.201	1.06703	222.156
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	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	233.287	1.06678	248.866
546	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	194.262	1.06671	207.222
547	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	194.346	1.06645	207.26
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]
551	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	194.347		207.261
552	crk-like protein. [swissprot;acc:p46109]	194.346		207.26
553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
556	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	194.368	1.06638	207.27
557	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	194.371	1.06637	207.272
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	144.041	1.06628	135.087
559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	194.452	1.06612	207.309
560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	193.021	1.06589	205.74
561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	193.183	1.06578	205.89
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	207.121	1.06577	220.744

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.