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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Value Type Gene description Rank Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 732 to 781 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 1215 218.268 212.916 1.02514
db83 protein. [swissprot;acc:p57088] 76 288 362 1.25694
dc11 protein. [refseq;acc:nm_020186] 2489 194.527 195.08 1.00284
dc12 protein. [refseq;acc:nm_020187] 2774 0.00001 0.00001 1
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 527 248.56 232.579 1.06871
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 1140 218.484 212.675 1.02731
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 1385 218.47 213.875 1.02148
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 1689 228.277 225.163 1.01383
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 634 226.523 213.786 1.05958
dead-box protein. [refseq;acc:nm_018665] 2012 193.517 191.766 1.00913
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] 1720 187.205 189.679 1.01322
defender against cell death 1 (dad-1). [swissprot;acc:p46966] 1740 206.595 209.258 1.01289
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 920 236.741 245.547 1.0372
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 2275 207.319 208.44 1.00541
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 217.392 218.498 1.00509
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 191.411 193.39 1.01034
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 2252 217.185 218.498 1.00605
delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 2097 214.979 213.39 1.00745
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 1178 218.186 212.672 1.02593
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 667 229.072 216.576 1.0577
deltex 2. [refseq;acc:nm_020892] 110 333.144 267.393 1.2459
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 111 332.925 267.274 1.24563
dendritic cell protein. [refseq;acc:nm_006360] 713 223.121 211.685 1.05402
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 267 241.07 267.88 1.11121
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 779 230.516 241.641 1.04826
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 2755 212.403 212.401 1.00001
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 322 86.7483 78.8995 1.09948
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 1430 187.114 190.925 1.02037
destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 2229 217.955 219.336 1.00634
developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295] 2762 0.00001 0.00001 1
developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039] 3092
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 174 335 286 1.17133
dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5] 3006 0.00001 0.00001 1
di-ras2. [refseq;acc:nm_017594] 892 212.028 204.055 1.03907
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 1591 225.119 228.769 1.01621
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 206.482 211.404 1.02384
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] 1039 207.719 214.236 1.03137
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 1462 205.817 209.851 1.0196
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 2392 214.966 215.799 1.00388
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 1009 229.116 221.823 1.03288
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 2213 210.127 211.475 1.00642
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 216.607 215.458 1.00533
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 216.608 215.456 1.00535
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] 2276 216.613 215.448 1.00541
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] 2289 216.605 215.46 1.00531
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] 2271 216.622 215.436 1.00551
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 1516 213.267 209.511 1.01793
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 395 218.827 238.407 1.08948
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 1515 213.267 209.511 1.01793
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 394 218.827 238.407 1.08948

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.
- http://analysis.yellowcouch.org/