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 1163 to 1212 of 3228 in total

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

Rank	description	red	green	network_comparison
1163	snare associated protein snapin. [refseq;acc:nm_012437]	220.758	215.097	1.02632
1164	transducin-like enhancer protein 4. [swissprot;acc:q04727]	219.438	213.818	1.02628
1165	transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726]	219.401	213.785	1.02627
1166	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	219.374	213.759
1167	homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	219.399	213.784	1.02626
1168	cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
1169	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]
1170	cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]
1171	hect type e3 ubiquitin ligase. [refseq;acc:nm_015052]
1172	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	219.375	213.767	1.02623
1173	candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822]	229.243	235.246	1.02619
1174	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579]	187.964	192.849	1.02599
1175	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449]	218.186	212.672	1.02593
1176	sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]
1177	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]
1178	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629]
1179	cellular modulator of immune recognition. [refseq;acc:nm_145021]
1180	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]
1181	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
1182	neurocalcin delta. [swissprot;acc:p29554]	225.104	230.931	1.02589
1183	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	225.103	230.928	1.02588
1184	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	216.729	222.334	1.02586
1185	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	225.094	230.913	1.02585
1186	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	218.402	212.904	1.02582
1187	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953]
1188	adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
1189	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	209.649	204.406	1.02565
1190	ubiquitin. [swissprot;acc:p02248]	209.6	204.372	1.02558
1191	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	220.742	215.237
1192	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]
1193	lbp-9. [refseq;acc:nm_014553]
1194	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]
1195	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	269.608	276.493	1.02554
1196	kinesin protein. [refseq;acc:nm_032559]	224.858	219.264	1.02551
1197	mstp028 protein. [refseq;acc:nm_031954]	219.042	213.6	1.02548
1198	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	269.59	276.454	1.02546
1199	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566]	241.496	235.508	1.02543
1200	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	219.03	213.604	1.0254
1201	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	210.986	216.344
1202	diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]	227.274	233.041	1.02537
1203	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829]	219.023	213.606	1.02536
1204	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	219.022	213.607	1.02535
1205	ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	224.805	219.251	1.02533
1206	integral membrane protein cii-3b. [sptrembl;acc:o75609]	207.646	212.891	1.02526
1207	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643]	207.644	212.888	1.02525
1208	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	224.878	219.342	1.02524
1209	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	207.931	213.175	1.02522
1210	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	224.764	219.241	1.02519
1211	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	214.364	219.759	1.02517
1212	kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]

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.