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 1844 to 1893 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1844	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [source:swissprot;acc:p26367]	214.773	212.417	1.01109	
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	214.702	1.01106	
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	214.698	1.01103	
1847	brain protein 16. [source:refseq;acc:nm_016458]	216.811	219.195	1.011	
1848	bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [source:refseq;acc:nm_001701]	218.441	216.064	1.011	
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	216.074	1.01097	
1850	adenylyl cyclase-associated protein 1 (cap 1). [source:swissprot;acc:q01518]	215.931	213.587	1.01097	
1851	peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [source:refseq;acc:nm_152331]	218.448	216.08	1.01096	
1852	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	196.008	198.154	1.01095	
1853	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	217.924	215.564	1.01095	
1854	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q13144]	222.215	224.637	1.0109	
1855	g-rich sequence factor-1 (grsf-1). [source:swissprot;acc:q12849]	217.891	215.542	1.0109	
1856	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [source:swissprot;acc:p31942]	217.892	215.543	1.0109	
1857	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9nr50]	222.215	224.637	1.0109	
1858	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [source:swissprot;acc:p52597]	217.893	215.545	1.01089	
1859	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [source:swissprot;acc:p31943]	217.895	215.547	1.01089	
1860	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [source:swissprot;acc:p55795]	217.895	215.547	1.01089	
1861	cytochrome b5 reductase b5r.2. [source:refseq;acc:nm_016229]	210.856	213.147	1.01087	
1862	cytochrome b5 reductase 1 (b5r.1). [source:refseq;acc:nm_016243]	210.856	213.147	1.01087	
1863	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [source:swissprot;acc:p00387]	210.856	213.147	1.01087	
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	200.89	1.01086	
1865	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [source:swissprot;acc:p41091]	221.639	224.046	1.01086	
1866	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9ui10]	221.725	224.133	1.01086	
1867	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [source:swissprot;acc:q13155]	203.071	200.89	1.01086	
1868	protein kinase nyd-sp25. [source:refseq;acc:nm_033516]	207.642	209.895	1.01085	
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	217.75	1.01082	
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	217.75	1.01082	
1871	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [source:swissprot;acc:o76031]	222.819	225.228	1.01081	
1872	dna polymerase delta p38 subunit. [source:refseq;acc:nm_015584]	222.819	225.228	1.01081	
1873	scratch; scratch 1. [source:refseq;acc:nm_031309]	210.55	208.305	1.01078	
1874	williams-beuren syndrome critical region protein 20 copy b. [source:refseq;acc:nm_145645]	223.862	226.271	1.01076	
1875	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [source:refseq;acc:nm_018044]	223.862	226.271	1.01076	
1876	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	223.862	226.271	1.01076	
1877	nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	212.186	214.467	1.01075	
1878	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	212.186	214.467	1.01075	
1879	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	212.186	214.467	1.01075	
1880	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [source:swissprot;acc:p32320]	220.852	223.225	1.01074	
1881	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	210.592	208.355	1.01074	
1882	60s ribosomal protein l28. [source:swissprot;acc:p46779]	215.896	213.61	1.0107	
1883	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	240.317	242.881	1.01067	
1884	putative gtp-binding protein ptd004 (pro2455). [source:swissprot;acc:q9ntk5]	215.081	217.373	1.01066	
1885	arginase 1 (ec 3.5.3.1) (liver-type arginase). [source:swissprot;acc:p05089]	204.44	206.615	1.01064	
1886	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [source:swissprot;acc:p78540]	204.512	206.682	1.01061	
1887	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [source:refseq;acc:nm_015077]	220.896	218.577	1.01061	
1888	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [source:swissprot;acc:q14197]	218.414	216.131	1.01056	
1889	rab3a interacting protein (rabin3)-like 1. [source:refseq;acc:nm_013401]	211.27	209.067	1.01054	
1890	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [source:refseq;acc:nm_022456]	211.314	209.111	1.01054	
1891	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [source:swissprot;acc:p25205]	233.828	231.395	1.01051	
1892	kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [source:swissprot;acc:q14145]	233.828	231.395	1.01051	
1893	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [source:refseq;acc:nm_013334]	222.842	225.17	1.01045	

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/