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 301 to 350 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
151	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Divided	55	46	1.19565
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Subtracted	226.582	198.444	28.138
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Divided	55	46	1.19565
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Subtracted	226.582	198.444	28.138
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Divided	249.663	298.263	1.19466
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Subtracted	226.582	198.444	28.138
154	musashi 2 isoform a. [refseq;acc:nm_138962]		227.491	199.458	28.033
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Divided	249.663	298.263	1.19466
155	musashi 1. [refseq;acc:nm_002442]	Subtracted	227.491	199.458	28.033
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Divided	249.663	298.263	1.19466
156	nuclear protein ukp68. [refseq;acc:nm_024824]	Subtracted	227.491	199.458	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	249.663	298.263	1.19466
157	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Subtracted	312	284	28
	transcription factor lbx1. [swissprot;acc:p52954]	Divided	249.663	298.263	1.19466
158	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Subtracted	312	284	28
	mosaic protein lgn. [swissprot;acc:p81274]	Divided	249.663	298.263	1.19466
159	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Subtracted	312	284	28
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Divided	249.663	298.263	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	312	284	28
161	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Divided	249.663	298.263	1.19466
162	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Subtracted	142	170	28
	nostrin. [refseq;acc:nm_052946]	Divided	209.299	249.187	1.19058
163	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Subtracted	133	105	28
	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Divided	209.299	249.187	1.19058
164	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Subtracted	133	105	28
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Divided	209.299	249.187	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	133	105	28
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Divided	209.299	249.187	1.19058
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Subtracted	312	284	28
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		133	105
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Divided	209.299	249.187	1.19058
168	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Subtracted	312	284	28
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Divided	82.5916	98.0548	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	312	284	28
170	huntingtin interacting protein c. [refseq;acc:nm_012272]		227.971	200.417	27.554
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Divided	227.199	192.715	1.17894
171	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]		227.202	192.823	1.17829
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Subtracted	201.478	228.784	27.306
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Divided	174.667	205.556	1.17685
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Subtracted	201.515	228.752	27.237
173	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Divided	227.032	193.056	1.17599
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		335	286	1.17133
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Subtracted	228.1	200.968	27.132
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Divided	199.949	234.187	1.17123
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Subtracted	228.085	201.006	27.079

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.