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 313 to 362 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
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
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Divided	205.556	174.667	1.17685
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Subtracted	228.752	201.515	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	193.056	227.032	1.17599
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		286	335	1.17133
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Subtracted	200.968	228.1	27.132
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Divided	234.187	199.949	1.17123
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Subtracted	201.006	228.085	27.079
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Divided	235.908	275.754	1.1689
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Subtracted	244.167	271.016	26.849
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Divided	196.695	229.406	1.1663
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Subtracted	267.88	241.07	26.81
178	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Divided	194.72	226.887	1.1652
179	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		194.79	226.884	1.16476
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Subtracted	254.15	227.357	26.793
180	pp3111 protein. [refseq;acc:nm_022156]
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	298.438	256.228	1.16474
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]		267.265	229.818	1.16294
	syntaxin 18. [swissprot;acc:q9p2w9]	Subtracted	254.15	227.357	26.793

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.