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	green	network_comparison

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Showing element 1001 to 1050 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Divided	238.704	255.68	1.07112
	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	Subtracted	237.28	252.492	15.212
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	Divided	238.704	255.68	1.07112
	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	Subtracted	237.28	252.492	15.212
503	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Divided	238.704	255.68	1.07112
504	homeobox protein barh-like 2. [swissprot;acc:q9umq3]	Subtracted	237.28	252.492	15.212
	oligophrenin 1. [swissprot;acc:o60890]	Divided	238.704	255.68	1.07112
505	ad24 protein. [refseq;acc:nm_022451]		251.334	234.672	1.071
	zinc finger protein t86. [swissprot;acc:o00488]	Subtracted	246.805	231.796	15.009
506	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]		215.237	230.07	14.833
	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	Divided	224.535	240.476	1.071
507	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	Subtracted	215.237	230.07	14.833
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	Divided	251.299	234.729	1.07059
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]		177.698	190.24	1.07058
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Subtracted	228.255	213.422	14.833
509	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Divided	177.698	190.239	1.07057
	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Subtracted	215.237	230.07	14.833
510	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Divided	177.699	190.24	1.07057
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]		250.053	233.725	1.06986
	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	Subtracted	214.754	229.565	14.811
512	block of proliferation 1. [swissprot;acc:q14137]	Divided	250.794	234.433	1.06979
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Subtracted	229.803	215.301	14.502
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Divided	218.596	204.344	1.06975
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Subtracted	227.483	212.994	14.489
514	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]		222.893	208.523	14.37
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Divided	218.613	204.382	1.06963
515	pescadillo homolog 1. [swissprot;acc:o00541]		251.297	234.941	1.06962
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Subtracted	248.463	234.095	14.368
516	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Divided	228.255	213.422	1.0695
517	metaxin 2. [swissprot;acc:o75431]		219.537	234.793	1.06949
	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Subtracted	248.463	234.095	14.368
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Divided	250.858	234.563	1.06947
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	218.596	204.344	14.252
519	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]		218.613	204.382	14.231
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Divided	218.702	204.582	1.06902
520	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Subtracted	223.356	209.149	14.207
	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	Divided	214.754	229.565	1.06897
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]		215.237	230.07	1.06891
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Subtracted	218.702	204.582	14.12
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Divided	222.893	208.523	1.06891
	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	Subtracted	229.709	215.631	14.078
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	Divided	215.237	230.07	1.06891
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Subtracted	247.47	233.441	14.029
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Divided	215.237	230.07	1.06891
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Subtracted	247.47	233.441	14.029
525	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	Divided	215.237	230.07	1.06891
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Subtracted	247.47	233.441	14.029

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.