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 2375 to 2424 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
1188	adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]	Divided	218.402	212.904	1.02582
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Subtracted	219.354	224.7	5.346
1189	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Divided	209.649	204.406	1.02565
	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	Subtracted	219.354	224.7	5.346
1190	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
	ubiquitin. [swissprot;acc:p02248]	Divided	209.6	204.372	1.02558
1191	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Subtracted	219.354	224.7	5.346
	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	Divided	220.742	215.237	1.02558
1192	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Subtracted	219.354	224.7	5.346
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Divided	220.742	215.237	1.02558
1193	lbp-9. [refseq;acc:nm_014553]
	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	Subtracted	219.354	224.7	5.346
1194	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]
	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]	Divided	220.742	215.237	1.02558
1195	espin. [refseq;acc:nm_031475]	Subtracted	219.354	224.7	5.346
	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	Divided	269.608	276.493	1.02554
1196	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]	Subtracted	219.354	224.7	5.346
	kinesin protein. [refseq;acc:nm_032559]	Divided	224.858	219.264	1.02551
1197	mstp028 protein. [refseq;acc:nm_031954]		219.042	213.6	1.02548
	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	Subtracted	219.354	224.7	5.346
1198	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	Divided	269.59	276.454	1.02546
1199	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]	Subtracted	219.354	224.7	5.346
	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566]	Divided	241.496	235.508	1.02543
1200	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Subtracted	219.354	224.699	5.345
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	Divided	219.03	213.604	1.0254
1201	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]	Subtracted	219.354	224.699	5.345
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Divided	210.986	216.344	1.0254
1202	diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]		227.274	233.041	1.02537
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Subtracted	219.354	224.699	5.345
1203	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829]	Divided	219.023	213.606	1.02536
1204	keratin associated protein 1.5. [refseq;acc:nm_031957]	Subtracted	219.354	224.699	5.345
	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	Divided	219.022	213.607	1.02535
1205	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Subtracted	219.354	224.699	5.345
	ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	Divided	224.805	219.251	1.02533
1206	integral membrane protein cii-3b. [sptrembl;acc:o75609]		207.646	212.891	1.02526
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Subtracted	219.354	224.699	5.345
1207	keratin associated protein 4.4. [refseq;acc:nm_032524]
	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]	Divided	207.644	212.888	1.02525
1208	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Subtracted	219.354	224.699	5.345
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Divided	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
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Subtracted	146.036	140.692	5.344
1210	keratin associated protein 9.2. [refseq;acc:nm_031961]		219.353	224.678	5.325
	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	Divided	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
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Subtracted	174.387	179.697	5.31
1212	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
	kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]	Divided	214.364	219.759	1.02517

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.