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 2351 to 2400 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
1176	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	Subtracted	214.364	219.759	5.395
	sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]	Divided	218.186	212.672	1.02593
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]
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Subtracted	214.364	219.759	5.395
1178	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629]	Divided	218.186	212.672	1.02593
	metaxin 1. [swissprot;acc:q13505]	Subtracted	199.552	204.925	5.373
1179	cellular modulator of immune recognition. [refseq;acc:nm_145021]	Divided	218.186	212.672	1.02593
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Subtracted	219.356	224.723	5.367
1180	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	5.358
	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]	Divided	218.186	212.672	1.02593
1181	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Subtracted	218.268	212.916	5.352
	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]	Divided	218.186	212.672	1.02593
1182	neurocalcin delta. [swissprot;acc:p29554]		225.104	230.931	1.02589
	retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338]	Subtracted	218.269	212.918	5.351
1183	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]		219.354	224.7	5.346
	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	Divided	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
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Subtracted	219.354	224.7	5.346
1185	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	Divided	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
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Subtracted	219.354	224.7	5.346
1187	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]
	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]	Divided	218.402	212.904	1.02582
1188	adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
	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

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.