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 325 to 374 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
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
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Divided	275.754	235.908	1.1689
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Subtracted	271.016	244.167	26.849
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Divided	229.406	196.695	1.1663
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Subtracted	241.07	267.88	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	226.887	194.72	1.1652
179	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		226.884	194.79	1.16476
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Subtracted	227.357	254.15	26.793
180	pp3111 protein. [refseq;acc:nm_022156]
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	256.228	298.438	1.16474
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]		229.818	267.265	1.16294
	syntaxin 18. [swissprot;acc:q9p2w9]	Subtracted	227.357	254.15	26.793
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Divided	277.546	240.461	1.15422
	rd protein. [swissprot;acc:p18615]	Subtracted	227.357	254.15	26.793
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Divided	228.306	198.011	1.153
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Subtracted	227.357	254.15	26.793
184	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Divided	274.027	237.79	1.15239
185	adiponectin receptor 2. [refseq;acc:nm_024551]		281.582	246.371	1.14292
	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Subtracted	227.357	254.15	26.793
186	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]	Divided	226.582	198.444	1.14179
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Subtracted	227.357	254.15	26.793
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Divided	226.582	198.444	1.14179
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Subtracted	227.357	254.15	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.