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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Value Type	Rank	Gene	Hugo	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1150 to 1199 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
1150	KCTD10	mstp028 protein. [refseq;acc:nm_031954]	5838.87	6355.06	1.08841
1151	ACTR1A	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	5322.74	5793.15	1.08838
1152	ACTR1B	beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
1153	SMARCB1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	5840.01	6355.56	1.08828
1154	TNFAIP1	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829]	5840.65	6355.84	1.08821
1155	TLE4	transducin-like enhancer protein 4. [swissprot;acc:q04727]	6270.67	6823.73	1.0882
1156	KCTD13	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	5840.77	6355.89	1.08819
1157	SHMT1	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	5418.33	5895.2	1.08801
1158	ALAD	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	5489.18	5972.09	1.08797
1159	DAGLB	kccr13l. [refseq;acc:nm_139179]	5538.8	6025.51	1.08787
1160	RAD51	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
1161	NAT5	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	5315.76	5782.63	1.08783
1162	NLK	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	5832.13	6343.59	1.0877
1163	ERC1	elks protein. [refseq;acc:nm_015064]
1164	SLC5A5	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	6600.36	7178.84	1.08764
1165	PRODH2	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	6604.44	7183.07	1.08761
1166	SLC5A8	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	6606.3	7185.01	1.0876
1167	SLC5A6	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	6607.68	7186.45	1.08759
1168	BUB3	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	5470.44	5949.49	1.08757
1169	ZNF207	zinc finger protein 207. [swissprot;acc:o43670]
1170	SUMO3	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	5826.34	6335.98	1.08747
1171	no value	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5826.29	6335.93
1172	ACRC	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	5826.32	6335.95
1173	CABC1	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	5799.35	6305.95	1.08735
1174	TATDN1	cda11 protein. [refseq;acc:nm_032026]	5874.11	6387.23
1175	ADCK2	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]	5799.35	6305.95
1176	ADCK4	aarf domain containing kinase 4. [refseq;acc:nm_024876]
1177	ADCK1	aarf domain containing kinase 1. [refseq;acc:nm_020421]
1178	no value	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	4392.63	4776.19	1.08732
1179	SLC20A2	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749]
1180	FDPS	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
1181	PCDH15	protocadherin 15 precursor. [swissprot;acc:q96qu1]
1182	SLC20A1	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
1183	LMBR1L	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
1184	GLI1	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
1185	SUFU	suppressor of fused. [refseq;acc:nm_016169]
1186	GLI3	zinc finger protein gli3. [swissprot;acc:p10071]
1187	LMBR1	limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
1188	PGC	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
1189	GLI2	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
1190	MAD2L1	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257]	6599.84	7174.29	1.08704
1191	ATP13A2	probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
1192	TBP	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]
1193	KIAA0664	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	5464.9	5940.16	1.08697
1194	CCT5	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	8425.35	7751.57	1.08692
1195	PARS2	similar to trna synthetase class ii. [refseq;acc:nm_152268]	5439.56	5911.24	1.08671
1196	no value	kappa b-ras 1. [refseq;acc:nm_020345]	5721.19	6217.2	1.0867
1197	NKIRAS2	i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595]
1198	SNAPAP	snare associated protein snapin. [refseq;acc:nm_012437]
1199	SHMT2	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	5449.48	5921.77	1.08667

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
- Hugo is the HGNC identifier if it exists
- 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.