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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Gene	Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	network_comparison	red

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Showing element 113 to 162 of 3228 in total

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

Rank	description	green	network_comparison	red
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	267.246	1.24557	332.874
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]
115	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	334.483	1.24545	268.565
117	neuralized-like. [refseq;acc:nm_004210]	266.948	1.24491	332.326
118	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	228.934	1.24382	284.753
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	259.004	1.23157	318.982
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	327.709	1.21699	269.278
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	327.655	1.2169	269.254
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	327.642	1.21688	269.248
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	327.601	1.21681	269.23
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	171.595	1.21519	208.52
125	high-mobility group 20a. [refseq;acc:nm_018200]	171.778	1.21429	208.588
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	114	1.21277	94
127	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
129	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]
130	protein hspc134 (protein cda04). [swissprot;acc:q9by43]
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]	242.562	1.21228	294.053
132	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	290	1.2069	350
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]	234.204	1.20493	194.372
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]	225.68	1.20415	271.752
140	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	49	1.20408	59
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]	319.651	1.20312	265.686
145	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	319.546	1.20293	265.639
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]	319.531	1.20291	265.632
147	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	42.3003	1.2009	50.7983
148	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	247.559	1.19841	296.677
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	170	1.19718	142
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	46	1.19565	55
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]	298.263	1.19466	249.663
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]	249.187	1.19058	209.299

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.