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 130 to 179 of 3228 in total

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

Rank	description	red	green	network_comparison
130	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	94	114	1.21277
131	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	294.053	242.562	1.21228
132	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	350	290	1.2069
133	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
135	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]
136	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
137	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]
138	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	194.372	234.204	1.20493
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	271.752	225.68	1.20415
140	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	59	49	1.20408
141	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	265.686	319.651	1.20312
145	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	265.639	319.546	1.20293
146	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	265.632	319.531	1.20291
147	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	50.7983	42.3003	1.2009
148	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	296.677	247.559	1.19841
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	142	170	1.19718
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	55	46	1.19565
151	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
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

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.