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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green

Results: HTML CSV LaTeX

Showing element 1825 to 1874 of 3228 in total

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

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

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/