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 1163 to 1212 of 3228 in total

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

Rank	description	red	green	network_comparison
1163	elks protein. [refseq;acc:nm_015064]	5832.13	6343.59	1.0877
1164	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	6600.36	7178.84	1.08764
1165	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	6604.44	7183.07	1.08761
1166	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	6606.3	7185.01	1.0876
1167	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	6607.68	7186.45	1.08759
1168	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	5470.44	5949.49	1.08757
1169	zinc finger protein 207. [swissprot;acc:o43670]
1170	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	5826.34	6335.98	1.08747
1171	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5826.29	6335.93
1172	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	5826.32	6335.95
1173	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	5799.35	6305.95	1.08735
1174	cda11 protein. [refseq;acc:nm_032026]	5874.11	6387.23
1175	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]	5799.35	6305.95
1176	aarf domain containing kinase 4. [refseq;acc:nm_024876]
1177	aarf domain containing kinase 1. [refseq;acc:nm_020421]
1178	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	4392.63	4776.19	1.08732
1179	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	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	protocadherin 15 precursor. [swissprot;acc:q96qu1]
1182	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
1183	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
1184	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
1185	suppressor of fused. [refseq;acc:nm_016169]
1186	zinc finger protein gli3. [swissprot;acc:p10071]
1187	limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
1188	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
1189	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
1190	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257]	6599.84	7174.29	1.08704
1191	probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
1192	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]
1193	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	5464.9	5940.16	1.08697
1194	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	8425.35	7751.57	1.08692
1195	similar to trna synthetase class ii. [refseq;acc:nm_152268]	5439.56	5911.24	1.08671
1196	kappa b-ras 1. [refseq;acc:nm_020345]	5721.19	6217.2	1.0867
1197	i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595]
1198	snare associated protein snapin. [refseq;acc:nm_012437]
1199	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	5449.48	5921.77	1.08667
1200	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	5950.27	6465.72	1.08663
1201	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	6042.31	6565.03	1.08651
1202	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	4913.07	5337.95	1.08648
1203	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749]	4322.65	4696.04	1.08638
1204	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	5946.33	6459.79	1.08635
1205	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
1206	asc-1 complex subunit p100. [refseq;acc:nm_032204]
1207	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]
1208	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	5913.73	6423.98	1.08628
1209	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814]	5420.87	5887.53	1.08609
1210	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6]	6410.73	6962.22	1.08603
1211	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
1212	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	4077.89	4428.28	1.08592

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.