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 1873 to 1922 of 3228 in total

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

Rank	description	red	green	network_comparison
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
1901	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	193.39
1902	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
1903	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	191.406	193.385
1904	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975]	191.424	193.404
1905	disrupter of silencing 10. [refseq;acc:nm_020368]	191.411	193.39
1906	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	191.41	193.389
1907	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	193.387
1908	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	191.415	193.394
1909	calmegin precursor. [swissprot;acc:o14967]	217.48	215.256	1.01033
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]
1913	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	215.745	213.564	1.01021
1914	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]
1915	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7]	215.747	213.571	1.01019
1916	rh type c glycoprotein. [refseq;acc:nm_016321]	196.88	198.88	1.01016
1917	p28 ing5. [refseq;acc:nm_032329]	215.848	218.039	1.01015
1918	endothelial-derived gene 1. [refseq;acc:nm_025205]	202.211	200.18
1919	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	187.231	185.349
1920	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	187.292	185.413	1.01013
1921	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707]	221.607	219.386	1.01012
1922	centaurin gamma 2. [swissprot;acc:q9upq3]	220.659	218.452	1.0101

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.