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

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Showing element 532 to 581 of 3228 in total

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

Rank	green	description	red	network_comparison
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]
551	194.347	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
552	194.346	crk-like protein. [swissprot;acc:p46109]	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	194.368	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	207.27	1.06638
557	194.371	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	207.272	1.06637
558	144.041	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	135.087	1.06628
559	194.452	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	207.309	1.06612
560	193.021	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	205.74	1.06589
561	193.183	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	205.89	1.06578
562	207.121	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	220.744	1.06577
563		calcyphosine. [swissprot;acc:q13938]
564		crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	121.261	sedlin. [swissprot;acc:o14582]	129.219	1.06563
566		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567		bet3 homolog. [swissprot;acc:o43617]
568	212.38	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	226.3	1.06554
569		t54 protein. [swissprot;acc:q92917]
570	215.631	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	229.709	1.06529
571	254.099	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	238.529	1.06528
572	213.945	cbf1 interacting corepressor. [refseq;acc:nm_004882]	227.86	1.06504
573		evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	208.264	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	221.807	1.06503
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	250.419	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	1.0648
577	210.944	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	224.606	1.06477
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	231.796	zinc finger protein t86. [swissprot;acc:o00488]	246.805	1.06475
580	252.038	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	236.751	1.06457
581	252.492	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	1.06411

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.