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

Results: HTML CSV LaTeX

Showing element 1851 to 1900 of 3228 in total

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

Rank	description	red	green	network_comparison
1851	peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331]	218.448	216.08	1.01096
1852	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	196.008	198.154	1.01095
1853	tubulin-tyrosine ligase. [refseq;acc:nm_153712]	217.924	215.564
1854	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	222.215	224.637	1.0109
1855	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	217.891	215.542
1856	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]	217.892	215.543
1857	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]	222.215	224.637
1858	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	217.893	215.545	1.01089
1859	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]	217.895	215.547
1860	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
1861	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	210.856	213.147	1.01087
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	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]	203.071	200.89	1.01086
1865	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	221.639	224.046
1866	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]	221.725	224.133
1867	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]	203.071	200.89
1868	protein kinase nyd-sp25. [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. [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). [refseq;acc:nm_006055]
1871	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	222.819	225.228	1.01081
1872	dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
1873	scratch; scratch 1. [refseq;acc:nm_031309]	210.55	208.305	1.01078
1874	williams-beuren syndrome critical region protein 20 copy b. [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. [refseq;acc:nm_018044]
1876	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
1877	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	212.186	214.467	1.01075
1878	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
1879	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]
1880	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [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). [sptrembl;acc:q9nq03]	210.592	208.355
1882	60s ribosomal protein l28. [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). [swissprot;acc:q01813]	240.317	242.881	1.01067
1884	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	215.081	217.373	1.01066
1885	arginase 1 (ec 3.5.3.1) (liver-type arginase). [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). [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. [refseq;acc:nm_015077]	220.896	218.577
1888	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197]	218.414	216.131	1.01056
1889	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	211.27	209.067	1.01054
1890	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]	211.314	209.111
1891	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205]	233.828	231.395	1.01051
1892	kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145]
1893	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334]	222.842	225.17	1.01045
1894	gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
1895	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	215.853	213.639	1.01036
1896	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290]	199.883	197.835	1.01035
1897	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
1898	lim/homeobox protein lhx4. [swissprot;acc:q969g2]	199.881	197.833
1899	lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]	199.884	197.837
1900	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	191.401	193.38	1.01034

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.