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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 1025 to 1074 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Divided	204.344	218.596	1.06975
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Subtracted	212.994	227.483	14.489
514	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]		208.523	222.893	14.37
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Divided	204.382	218.613	1.06963
515	pescadillo homolog 1. [swissprot;acc:o00541]		234.941	251.297	1.06962
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Subtracted	234.095	248.463	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	213.422	228.255	1.0695
517	metaxin 2. [swissprot;acc:o75431]		234.793	219.537	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	234.095	248.463	14.368
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Divided	234.563	250.858	1.06947
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	204.344	218.596	14.252
519	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]		204.382	218.613	14.231
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Divided	204.582	218.702	1.06902
520	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Subtracted	209.149	223.356	14.207
	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	Divided	229.565	214.754	1.06897
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]		230.07	215.237	1.06891
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Subtracted	204.582	218.702	14.12
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Divided	208.523	222.893	1.06891
	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	Subtracted	215.631	229.709	14.078
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	Divided	230.07	215.237	1.06891
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Subtracted	233.441	247.47	14.029
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Divided	230.07	215.237	1.06891
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Subtracted	233.441	247.47	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	230.07	215.237	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	233.441	247.47	14.029
526	histone h2b. [refseq;acc:nm_175055]
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	Divided	234.401	250.538	1.06884
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]		232.579	248.56	1.06871
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Subtracted	233.441	247.47	14.029
528	histone h2b.d (h2b/d). [swissprot;acc:q99877]
	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	Divided	237.393	222.146	1.06864
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]		235.506	251.653	1.06856
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Subtracted	233.441	247.47	14.029
530	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Divided	212.994	227.483	1.06803
531	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Subtracted	233.441	247.47	14.029
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Divided	209.149	223.356	1.06793
532	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Subtracted	126	112	14
	zinc finger-like protein 9. [refseq;acc:nm_033414]	Divided	235.004	250.942	1.06782
533	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	44	58	14
	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	Divided	235.004	250.942	1.06782
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	44	58	14
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	Divided	252.708	236.662	1.0678
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Subtracted	126	112	14
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Divided	227.136	242.531	1.06778
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Subtracted	126	112	14
537	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		24	10
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Divided	215.301	229.803	1.06736

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.