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	network_comparison	green

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Showing element 530 to 579 of 3228 in total

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

Rank	description	red	network_comparison	green
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	227.483	1.06803	212.994
531	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	223.356	1.06793	209.149
532	zinc finger-like protein 9. [refseq;acc:nm_033414]	250.942	1.06782	235.004
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	1.0678	252.708
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	242.531	1.06778	227.136
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	229.803	1.06736	215.301
538	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	253.604
539	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	236.964	1.06708	252.86
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	222.156	1.06703	208.201
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]	248.866	1.06678	233.287
546	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	207.222	1.06671	194.262
547	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	207.26	1.06645	194.346
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]	207.261		194.347
552	crk-like protein. [swissprot;acc:p46109]	207.26		194.346
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]	207.27	1.06638	194.368
557	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	207.272	1.06637	194.371
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	135.087	1.06628	144.041
559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	207.309	1.06612	194.452
560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	205.74	1.06589	193.021
561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	205.89	1.06578	193.183
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	220.744	1.06577	207.121
563	calcyphosine. [swissprot;acc:q13938]
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	sedlin. [swissprot;acc:o14582]	129.219	1.06563	121.261
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567	bet3 homolog. [swissprot;acc:o43617]
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	226.3	1.06554	212.38
569	t54 protein. [swissprot;acc:q92917]
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	229.709	1.06529	215.631
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	238.529	1.06528	254.099
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	227.86	1.06504	213.945
573	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	221.807	1.06503	208.264
575	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	1.0648	250.419
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	224.606	1.06477	210.944
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
579	zinc finger protein t86. [swissprot;acc:o00488]	246.805	1.06475	231.796

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.