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

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Showing element 2380 to 2429 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
1190	ubiquitin. [swissprot;acc:p02248]	Divided	204.372	209.6	1.02558
1191	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Subtracted	224.7	219.354	5.346
	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	Divided	215.237	220.742	1.02558
1192	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Subtracted	224.7	219.354	5.346
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Divided	215.237	220.742	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	224.7	219.354	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	215.237	220.742	1.02558
1195	espin. [refseq;acc:nm_031475]	Subtracted	224.7	219.354	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	276.493	269.608	1.02554
1196	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]	Subtracted	224.7	219.354	5.346
	kinesin protein. [refseq;acc:nm_032559]	Divided	219.264	224.858	1.02551
1197	mstp028 protein. [refseq;acc:nm_031954]		213.6	219.042	1.02548
	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	Subtracted	224.7	219.354	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	276.454	269.59	1.02546
1199	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]	Subtracted	224.7	219.354	5.346
	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566]	Divided	235.508	241.496	1.02543
1200	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Subtracted	224.699	219.354	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	213.604	219.03	1.0254
1201	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]	Subtracted	224.699	219.354	5.345
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Divided	216.344	210.986	1.0254
1202	diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]		233.041	227.274	1.02537
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Subtracted	224.699	219.354	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	213.606	219.023	1.02536
1204	keratin associated protein 1.5. [refseq;acc:nm_031957]	Subtracted	224.699	219.354	5.345
	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	Divided	213.607	219.022	1.02535
1205	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Subtracted	224.699	219.354	5.345
	ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	Divided	219.251	224.805	1.02533
1206	integral membrane protein cii-3b. [sptrembl;acc:o75609]		212.891	207.646	1.02526
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Subtracted	224.699	219.354	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	212.888	207.644	1.02525
1208	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Subtracted	224.699	219.354	5.345
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Divided	219.342	224.878	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]		213.175	207.931	1.02522
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Subtracted	140.692	146.036	5.344
1210	keratin associated protein 9.2. [refseq;acc:nm_031961]		224.678	219.353	5.325
	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	Divided	219.241	224.764	1.02519
1211	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]		219.759	214.364	1.02517
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Subtracted	179.697	174.387	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	219.759	214.364	1.02517
1213	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]	Subtracted	179.697	174.387	5.31
	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	Divided	219.759	214.364	1.02517
1214	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]	Subtracted	179.697	174.387	5.31
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Divided	219.759	214.364	1.02517
1215	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]		212.916	218.268	1.02514

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.