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 1180 to 1229 of 3228 in total

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

Rank	description	red	green	network_comparison
1180	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]	218.186	212.672	1.02593
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]
1213	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
1214	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]
1215	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	218.268	212.916	1.02514
1216	retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338]	218.269	212.918	1.02513
1217	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292]	211.959	217.258	1.025
1218	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
1219	coactosin-like protein. [swissprot;acc:q14019]
1220	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]
1221	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]
1222	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	206.774	211.936	1.02496
1223	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	206.771	211.926	1.02493
1224	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	225.906	231.524	1.02487
1225	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	166.846	170.989	1.02483
1226	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]
1227	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	172.365	168.219	1.02465
1228	glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507]	213.079	218.325	1.02462
1229	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506]

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.