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	green	red	network_comparison

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Showing element 293 to 342 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
147	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Subtracted	267.842	239.32	28.522
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	42.3003	50.7983	1.2009
148	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Subtracted	198.444	226.582	28.138
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	247.559	296.677	1.19841
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		170	142	1.19718
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Subtracted	198.444	226.582	28.138
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided	46	55	1.19565
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Subtracted	198.444	226.582	28.138
151	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Divided	46	55	1.19565
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Subtracted	198.444	226.582	28.138
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Divided	46	55	1.19565
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Subtracted	198.444	226.582	28.138
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Divided	298.263	249.663	1.19466
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Subtracted	198.444	226.582	28.138
154	musashi 2 isoform a. [refseq;acc:nm_138962]		199.458	227.491	28.033
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Divided	298.263	249.663	1.19466
155	musashi 1. [refseq;acc:nm_002442]	Subtracted	199.458	227.491	28.033
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Divided	298.263	249.663	1.19466
156	nuclear protein ukp68. [refseq;acc:nm_024824]	Subtracted	199.458	227.491	28.033
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Divided	298.263	249.663	1.19466
157	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Subtracted	284	312	28
	transcription factor lbx1. [swissprot;acc:p52954]	Divided	298.263	249.663	1.19466
158	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Subtracted	284	312	28
	mosaic protein lgn. [swissprot;acc:p81274]	Divided	298.263	249.663	1.19466
159	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Subtracted	284	312	28
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Divided	298.263	249.663	1.19466
160	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Subtracted	284	312	28
161	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Divided	298.263	249.663	1.19466
162	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Subtracted	170	142	28
	nostrin. [refseq;acc:nm_052946]	Divided	249.187	209.299	1.19058
163	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Subtracted	105	133	28
	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Divided	249.187	209.299	1.19058
164	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Subtracted	105	133	28
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Divided	249.187	209.299	1.19058
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	105	133	28
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Divided	249.187	209.299	1.19058
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Subtracted	284	312	28
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		105	133
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Divided	249.187	209.299	1.19058
168	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Subtracted	284	312	28
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Divided	98.0548	82.5916	1.18722
169	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Subtracted	284	312	28
170	huntingtin interacting protein c. [refseq;acc:nm_012272]		200.417	227.971	27.554
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Divided	192.715	227.199	1.17894
171	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]		192.823	227.202	1.17829
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Subtracted	228.784	201.478	27.306

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.