Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type description Network Comparison Type Interaction Map Filtered green 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	description	green	red	network_comparison	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	255.68	238.704	1.07112	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	255.68	238.704	1.07112	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	255.68	238.704	1.07112	
504	oligophrenin 1. [source:swissprot;acc:o60890]	255.68	238.704	1.07112	
505	ad24 protein. [source:refseq;acc:nm_022451]	234.672	251.334	1.071	
506	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	240.476	224.535	1.071	
507	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	234.729	251.299	1.07059	
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	190.24	177.698	1.07058	
509	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	190.239	177.698	1.07057	
510	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	190.24	177.699	1.07057	
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	233.725	250.053	1.06986	
512	block of proliferation 1. [source:swissprot;acc:q14137]	234.433	250.794	1.06979	
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	204.344	218.596	1.06975	
514	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	204.382	218.613	1.06963	
515	pescadillo homolog 1. [source:swissprot;acc:o00541]	234.941	251.297	1.06962	
516	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	213.422	228.255	1.0695	
517	metaxin 2. [source:swissprot;acc:o75431]	234.793	219.537	1.06949	
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	234.563	250.858	1.06947	
519	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	204.582	218.702	1.06902	
520	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	229.565	214.754	1.06897	
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	230.07	215.237	1.06891	
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	208.523	222.893	1.06891	
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	230.07	215.237	1.06891	
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	230.07	215.237	1.06891	
525	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	230.07	215.237	1.06891	
526	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	234.401	250.538	1.06884	
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	232.579	248.56	1.06871	
528	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	237.393	222.146	1.06864	
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	235.506	251.653	1.06856	
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	212.994	227.483	1.06803	
531	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	209.149	223.356	1.06793	
532	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	235.004	250.942	1.06782	
533	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	235.004	250.942	1.06782	
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	235.004	250.942	1.06782	
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	252.708	236.662	1.0678	
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	227.136	242.531	1.06778	
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	215.301	229.803	1.06736	
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	253.604	237.627	1.06724	
539	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	252.86	236.964	1.06708	
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	208.201	222.156	1.06703	
541	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	208.201	222.156	1.06703	
542	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	208.201	222.156	1.06703	
543	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	208.201	222.156	1.06703	
544	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	208.201	222.156	1.06703	
545	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	233.287	248.866	1.06678	
546	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	194.262	207.222	1.06671	
547	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	194.346	207.26	1.06645	
548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	194.346	207.26	1.06645	
549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	194.346	207.26	1.06645	
550	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	194.346	207.26	1.06645	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/