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

Results: HTML CSV LaTeX

Showing element 1144 to 1193 of 3228 in total

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

Rank	description	red	green	network_comparison
1144	cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]	6281.21	6837.61	1.08858
1145	40s ribosomal protein s30. [swissprot;acc:q05472]	5893.97	6416.07
1146	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	6281.21	6837.61
1147	cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]
1148	hect type e3 ubiquitin ligase. [refseq;acc:nm_015052]
1149	transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726]	6280.74	6837.01	1.08857
1150	mstp028 protein. [refseq;acc:nm_031954]	5838.87	6355.06	1.08841
1151	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	5322.74	5793.15	1.08838
1152	beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
1153	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	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829]	5840.65	6355.84	1.08821
1155	transducin-like enhancer protein 4. [swissprot;acc:q04727]	6270.67	6823.73	1.0882
1156	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	5840.77	6355.89	1.08819
1157	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	5418.33	5895.2	1.08801
1158	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	5489.18	5972.09	1.08797
1159	kccr13l. [refseq;acc:nm_139179]	5538.8	6025.51	1.08787
1160	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
1161	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	5315.76	5782.63	1.08783
1162	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	5832.13	6343.59	1.0877
1163	elks protein. [refseq;acc:nm_015064]
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

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.