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

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

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.