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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 2151 to 2200 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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	
1084	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [source:swissprot;acc:o95674]	Divided	6437.49	7029.22	1.09192	
1085	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Divided	6520.28	7119.28	1.09187	
1085	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [source:swissprot;acc:q13162]	Subtracted	6343.26	6862.94	519.68	
1086	dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [source:swissprot;acc:q99518]	Subtracted	5365.06	5884.52	519.46	
1086	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Divided	6520.28	7119.28	1.09187	
1087	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	Divided	5732.73	6256.63	1.09139	
1087	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	Subtracted	6439.79	6959.21	519.42	
1088	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	Subtracted	6439.79	6959.21	519.42	
1088	tax interaction protein 1. [source:refseq;acc:nm_014604]	Divided	5732.73	6256.63	1.09139	
1089	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	Subtracted	6439.79	6959.21	519.42	
1089	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [source:swissprot;acc:p21549]	Divided	6390.28	6973.08	1.0912	
1090	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	Subtracted	6439.79	6959.21	519.42	
1090	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Divided	5651.07	6164.55	1.09086	
1091	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [source:swissprot;acc:q92871]	Subtracted	5509.89	6029.29	519.4	
1091	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	Divided	5791.05	6316.61	1.09075	
1092	dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [source:swissprot;acc:q01740]	Subtracted	5365.14	5884.43	519.29	
1092	hskin17 protein. [source:refseq;acc:nm_012311]	Divided	5791.05	6316.61	1.09075	
1093	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	Divided	5791.05	6316.61	1.09075	
1093	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [source:swissprot;acc:p31512]	Subtracted	5365.22	5884.32	519.1	
1094	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	Subtracted	5795.13	6314.19	519.06	
1094	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]	Divided	5791.05	6316.61	1.09075	
1095	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Subtracted	4115.39	4633.96	518.57	
1095	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	Divided	5791.05	6316.61	1.09075	
1096	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	Subtracted	6334.15	6852.61	518.46	
1096	kinesin protein. [source:refseq;acc:nm_032559]	Divided	5356.23	5842.15	1.09072	
1097	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Subtracted	4708.61	5226.71	518.1	
1097	homolog of yeast maf1. [source:refseq;acc:nm_032272]	Divided	6133.83	6690.18	1.0907	
1098	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Subtracted	4708.61	5226.71	518.1	
1098	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	Divided	6133.83	6690.18	1.0907	
1099	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Subtracted	4708.61	5226.71	518.1	
1099	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	Divided	6133.83	6690.18	1.0907	
1100	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Subtracted	4708.61	5226.71	518.1	
1100	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	Divided	6133.83	6690.18	1.0907	

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/