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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Gene description Value Type Rank Filtered Network Comparison Type Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 851 to 900 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
network_comparison
green
red
dc11 protein. [refseq;acc:nm_020186] 2489 1 1.00284 195.08 194.527
dc12 protein. [refseq;acc:nm_020187] 2774 1 0.00001 0.00001
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 527 1.06871 232.579 248.56
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 1140 1.02731 212.675 218.484
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 372 0 1.04489 12402.7 11869.9
1385 1 1.02148 213.875 218.47
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 1689 1.01383 225.163 228.277
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 176 0 1.13359 11528 13068
634 1 1.05958 213.786 226.523
dead-box protein. [refseq;acc:nm_018665] 58 0 1.36296 14486 10628.3
2012 1 1.00913 191.766 193.517
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 326 0 1.05779 11295.6 11948.4
1720 1 1.01322 189.679 187.205
defender against cell death 1 (dad-1). [swissprot;acc:p46966] 1740 1.01289 209.258 206.595
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 920 1.0372 245.547 236.741
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 2275 1.00541 208.44 207.319
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] 2305 1.00509 218.498 217.392
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] 1901 1.01034 193.39 191.411
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 2252 1.00605 218.498 217.185
delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 2097 1.00745 213.39 214.979
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 1178 1.02593 212.672 218.186
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 667 1.0577 216.576 229.072
deltex 2. [refseq;acc:nm_020892] 110 1.2459 267.393 333.144
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 80 0 1.27636 11617.9 9102.34
111 1 1.24563 267.274 332.925
dendritic cell protein. [refseq;acc:nm_006360] 713 1.05402 211.685 223.121
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 267 1.11121 267.88 241.07
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 779 1.04826 241.641 230.516
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 2755 1.00001 212.401 212.403
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 322 1.09948 78.8995 86.7483
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 1430 1.02037 190.925 187.114
destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 2229 1.00634 219.336 217.955
developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295] 2762 1 0.00001 0.00001
developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039] 3092
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 174 1.17133 286 335
dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5] 3006 1 0.00001 0.00001
di-ras2. [refseq;acc:nm_017594] 892 1.03907 204.055 212.028
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 164 0 1.14975 10412.4 11971.7
1591 1 1.01621 228.769 225.119
dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 1298 1.02384 211.404 206.482
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] 1039 1.03137 214.236 207.719
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 1462 1.0196 209.851 205.817
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 2392 1.00388 215.799 214.966
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 344 0 1.05116 10027.6 10540.6
1009 1 1.03288 221.823 229.116
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 2213 1.00642 211.475 210.127
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] 2288 1.00533 215.458 216.607
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] 2286 1.00535 215.456 216.608
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 103 0 1.21815 9130.38 7495.26
2276 1 1.00541 215.448 216.613

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.
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