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 2118 to 2167 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1059	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [source:swissprot;acc:q15814]	Divided	5719.01	6248.6	1.0926	
1060	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	Subtracted	5791.05	6316.61	525.56	
1060	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	Divided	5719.01	6248.6	1.0926	
1061	hskin17 protein. [source:refseq;acc:nm_012311]	Subtracted	5791.05	6316.61	525.56	
1061	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	Divided	5412.23	5913.4	1.0926	
1062	ammecr1 protein. [source:refseq;acc:nm_015365]	Divided	5412.23	5913.4	1.0926	
1062	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	Subtracted	5791.05	6316.61	525.56	
1063	mrna-associated protein mrnp 41 (rae1 protein homolog). [source:swissprot;acc:p78406]	Divided	5412.23	5913.4	1.0926	
1063	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [source:swissprot;acc:q13310]	Subtracted	5791.05	6316.61	525.56	
1064	dead-box protein. [source:refseq;acc:nm_018665]	Divided	5719.01	6248.6	1.0926	
1064	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	Subtracted	5791.05	6316.61	525.56	
1065	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	Subtracted	6350.81	6874.88	524.07	
1065	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [source:swissprot;acc:p27695]	Divided	6393.81	6984.94	1.09245	
1066	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	Subtracted	5732.73	6256.63	523.9	
1066	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	Divided	5417.06	5917.79	1.09244	
1067	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [source:swissprot;acc:q15031]	Divided	5417.07	5917.79	1.09243	
1067	tax interaction protein 1. [source:refseq;acc:nm_014604]	Subtracted	5732.73	6256.63	523.9	
1068	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	Subtracted	5857.48	6380.4	522.92	
1068	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	Divided	6201.54	6774.35	1.09237	
1069	elongation factor 2 (ef-2). [source:swissprot;acc:p13639]	Divided	5494.73	6001.08	1.09215	
1069	glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	Subtracted	6251.32	6774.12	522.8	
1070	metabotropic glutamate receptor 2 precursor (mglur2). [source:swissprot;acc:q14416]	Divided	5494.73	6001.08	1.09215	
1070	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	Subtracted	6042.31	6565.03	522.72	
1071	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Subtracted	5893.97	6416.07	522.1	
1071	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	Divided	5494.73	6001.08	1.09215	
1072	electron transfer flavoprotein beta-subunit (beta-etf). [source:swissprot;acc:p38117]	Subtracted	7794.41	8316.04	521.63	
1072	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Divided	5207.39	5687.2	1.09214	
1073	dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [source:swissprot;acc:p49326]	Subtracted	5364.3	5885.48	521.18	
1073	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Divided	5207.39	5687.2	1.09214	
1074	putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [source:swissprot;acc:o60774]	Subtracted	5364.3	5885.48	521.18	
1074	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Divided	5207.39	5687.2	1.09214	
1075	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	Subtracted	4359.82	4880.99	521.17	
1075	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	Divided	6441.56	7034.86	1.09211	
1076	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Subtracted	4565.34	5085.92	520.58	
1076	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	Divided	6439.63	7032.19	1.09202	
1077	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	Subtracted	4565.34	5085.92	520.58	
1077	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	Divided	6439.66	7032.22	1.09202	
1078	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	Subtracted	4565.34	5085.92	520.58	
1078	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	Divided	6439.63	7032.19	1.09202	
1079	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [source:swissprot;acc:o75380]	Subtracted	4565.34	5085.92	520.58	
1079	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	Divided	6439.66	7032.22	1.09202	
1080	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [source:swissprot;acc:p14649]	Subtracted	4565.34	5085.92	520.58	
1080	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	Divided	6439.3	7031.73	1.092	
1081	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Subtracted	4565.34	5085.92	520.58	
1081	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	Divided	6439.3	7031.73	1.092	
1082	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Subtracted	5364.77	5884.89	520.12	
1082	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	Divided	6439.35	7031.8	1.092	
1083	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	Divided	6213.51	6785.04	1.09198	
1083	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [source:swissprot;acc:o15305]	Subtracted	5511.96	6031.95	519.99	
1084	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [source:swissprot;acc:p30566]	Subtracted	7444.28	7964	519.72	

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/