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

Results: HTML CSV LaTeX

Showing element 1825 to 1874 of 3228 in total

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

Rank	green	description	network_comparison	red
1825	200.086	fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]	1.0115	202.386
1826	200.094	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	1.01149	202.393
1827	189.219	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	1.01147	191.39
1828	200.115	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]		202.41
1829	215.323	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708]	1.01146	212.884
1830	243.069	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237]	1.01144	240.32
1831	212.328	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	1.01139	214.746
1832	182.459	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	1.01136	180.409
1833		cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
1834		catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
1835	192.396	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	1.01132	194.573
1836	211.17	ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247]	1.01125	208.821
1837	221.446	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	1.01124	218.984
1838		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
1839	224.001	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	1.01118	221.525
1840	209.544	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695]	1.01116	211.882
1841	210.113	presenilins associated rhomboid-like protein. [refseq;acc:nm_018622]	1.01115	212.455
1842		gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
1843		potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
1844	212.417	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367]	1.01109	214.773
1845	214.702	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]	1.01106	217.077
1846	214.698	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470]	1.01103	217.066
1847	219.195	brain protein 16. [refseq;acc:nm_016458]	1.011	216.811
1848	216.064	bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701]		218.441
1849	216.074	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	1.01097	218.445
1850	213.587	adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518]		215.931
1851	216.08	peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331]	1.01096	218.448
1852	198.154	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	1.01095	196.008
1853	215.564	tubulin-tyrosine ligase. [refseq;acc:nm_153712]		217.924
1854	224.637	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	1.0109	222.215
1855	215.542	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]		217.891
1856	215.543	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]		217.892
1857	224.637	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]		222.215
1858	215.545	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	1.01089	217.893
1859	215.547	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]		217.895
1860		heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
1861	213.147	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	1.01087	210.856
1862		cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
1863		nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
1864	200.89	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	1.01086	203.071
1865	224.046	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]		221.639
1866	224.133	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]		221.725
1867	200.89	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]		203.071
1868	209.895	protein kinase nyd-sp25. [refseq;acc:nm_033516]	1.01085	207.642
1869	217.75	lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697]	1.01082	220.107
1870		lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]
1871	225.228	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	1.01081	222.819
1872		dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
1873	208.305	scratch; scratch 1. [refseq;acc:nm_031309]	1.01078	210.55
1874	226.271	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	1.01076	223.862

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.