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

Results: HTML CSV LaTeX

Showing element 1863 to 1912 of 3228 in total

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

Rank	green	description	network_comparison	red
1863	213.147	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	1.01087	210.856
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
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	214.467	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	1.01075	212.186
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	223.225	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320]	1.01074	220.852
1881	208.355	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		210.592
1882	213.61	60s ribosomal protein l28. [swissprot;acc:p46779]	1.0107	215.896
1883	242.881	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]	1.01067	240.317
1884	217.373	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	1.01066	215.081
1885	206.615	arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089]	1.01064	204.44
1886	206.682	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540]	1.01061	204.512
1887	218.577	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077]		220.896
1888	216.131	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197]	1.01056	218.414
1889	209.067	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	1.01054	211.27
1890	209.111	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]		211.314
1891	231.395	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205]	1.01051	233.828
1892		kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145]
1893	225.17	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334]	1.01045	222.842
1894		gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
1895	213.639	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	1.01036	215.853
1896	197.835	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290]	1.01035	199.883
1897		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
1898	197.833	lim/homeobox protein lhx4. [swissprot;acc:q969g2]		199.881
1899	197.837	lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]		199.884
1900	193.38	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	1.01034	191.401
1901	193.39	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]		191.411
1902		lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
1903	193.385	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]		191.406
1904	193.404	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975]		191.424
1905	193.39	disrupter of silencing 10. [refseq;acc:nm_020368]		191.411
1906	193.389	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]		191.41
1907	193.387	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]		191.408
1908	193.394	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]		191.415
1909	215.256	calmegin precursor. [swissprot;acc:o14967]	1.01033	217.48
1910		calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824]
1911		soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]
1912		rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]

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.