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

Results: HTML CSV LaTeX

Showing element 151 to 200 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
151	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	55	46	1.19565
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	249.663	298.263	1.19466
154	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]
155	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]
156	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]
157	transcription factor lbx1. [swissprot;acc:p52954]
158	mosaic protein lgn. [swissprot;acc:p81274]
159	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]
160	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
161	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]
162	nostrin. [refseq;acc:nm_052946]	209.299	249.187	1.19058
163	eap30 subunit of ell complex. [refseq;acc:nm_007241]
164	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]
167	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
168	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	82.5916	98.0548	1.18722
169	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	227.199	192.715	1.17894
171	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	227.202	192.823	1.17829
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	174.667	205.556	1.17685
173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	227.032	193.056	1.17599
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	335	286	1.17133
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	199.949	234.187	1.17123
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	275.754	235.908	1.1689
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	229.406	196.695	1.1663
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	226.887	194.72	1.1652
179	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	226.884	194.79	1.16476
180	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	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
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	277.546	240.461	1.15422
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	228.306	198.011	1.153
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	274.027	237.79	1.15239
185	adiponectin receptor 2. [refseq;acc:nm_024551]	281.582	246.371	1.14292
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]	226.582	198.444	1.14179
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
192	musashi 2 isoform a. [refseq;acc:nm_138962]	227.491	199.458	1.14055
193	musashi 1. [refseq;acc:nm_002442]
194	nuclear protein ukp68. [refseq;acc:nm_024824]
195	huntingtin interacting protein c. [refseq;acc:nm_012272]	227.971	200.417	1.13748
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	263.215	231.407	1.13745
197	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	263.191	231.394	1.13741
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	242.735	276.059	1.13729
200	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	242.718	276.018	1.1372

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.