Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 1162 to 1211 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1162	nemo-like kinase; likely ortholog of mouse nemo like kinase. [source:refseq;acc:nm_016231]	5832.13	6343.59	1.0877	
1163	elks protein. [source:refseq;acc:nm_015064]	5832.13	6343.59	1.0877	
1164	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	6600.36	7178.84	1.08764	
1165	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	6604.44	7183.07	1.08761	
1166	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	6606.3	7185.01	1.0876	
1167	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	6607.68	7186.45	1.08759	
1168	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	5470.44	5949.49	1.08757	
1169	zinc finger protein 207. [source:swissprot;acc:o43670]	5470.44	5949.49	1.08757	
1170	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	5826.34	6335.98	1.08747	
1171	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	5826.29	6335.93	1.08747	
1172	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	5826.32	6335.95	1.08747	
1173	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	5799.35	6305.95	1.08735	
1174	cda11 protein. [source:refseq;acc:nm_032026]	5874.11	6387.23	1.08735	
1175	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	5799.35	6305.95	1.08735	
1176	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	5799.35	6305.95	1.08735	
1177	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	5799.35	6305.95	1.08735	
1178	pepsin a precursor (ec 3.4.23.1). [source: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. [source:refseq;acc:nm_006749]	4392.63	4776.19	1.08732	
1180	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	4392.63	4776.19	1.08732	
1181	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	4392.63	4776.19	1.08732	
1182	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	4392.63	4776.19	1.08732	
1183	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	4392.63	4776.19	1.08732	
1184	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	4392.63	4776.19	1.08732	
1185	suppressor of fused. [source:refseq;acc:nm_016169]	4392.63	4776.19	1.08732	
1186	zinc finger protein gli3. [source:swissprot;acc:p10071]	4392.63	4776.19	1.08732	
1187	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	4392.63	4776.19	1.08732	
1188	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	4392.63	4776.19	1.08732	
1189	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	4392.63	4776.19	1.08732	
1190	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [source:swissprot;acc:q13257]	6599.84	7174.29	1.08704	
1191	probable cation-transporting atpase 1 (ec 3.6.1.-). [source:swissprot;acc:q9nq11]	6599.84	7174.29	1.08704	
1192	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [source:swissprot;acc:p20226]	6599.84	7174.29	1.08704	
1193	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [source:swissprot;acc:o75153]	5464.9	5940.16	1.08697	
1194	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	8425.35	7751.57	1.08692	
1195	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	5439.56	5911.24	1.08671	
1196	kappa b-ras 1. [source:refseq;acc:nm_020345]	5721.19	6217.2	1.0867	
1197	i-kappa-b-interacting ras-like protein 2. [source:refseq;acc:nm_017595]	5721.19	6217.2	1.0867	
1198	snare associated protein snapin. [source:refseq;acc:nm_012437]	5721.19	6217.2	1.0867	
1199	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	5449.48	5921.77	1.08667	
1200	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	5950.27	6465.72	1.08663	
1201	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source: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). [source: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)]. [source: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). [source:swissprot;acc:o15524]	5946.33	6459.79	1.08635	
1205	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	5946.33	6459.79	1.08635	
1206	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	5946.33	6459.79	1.08635	
1207	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	5946.33	6459.79	1.08635	
1208	meiotic recombination protein dmc1/lim15 homolog. [source: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)]. [source: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). [source:swissprot;acc:q9nvh6]	6410.73	6962.22	1.08603	
1211	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	6410.73	6962.22	1.08603	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/