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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7141 to 7190 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
893 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Ranked Divided 227.585 219.037 1.03903
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Squared Subtracted 22623.7 26336.8 3713.1
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Measured 6599.84 7174.29 574.45
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Squared Divided 26312 30514.1 1.1597
894 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Ranked Subtracted 231.163 239.205 8.042
parafibromin. [refseq;acc:nm_024529] Measured Divided 4331.17 4771.22 1.1016
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Ranked 217.491 209.323 1.03902
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Squared 20322.5 23567.1 1.15966
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Measured Subtracted 6599.84 7174.29 574.45
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Rooted Divided 56.2142 59.6282 1.06073
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared Subtracted 23242.1 26955.1 3713
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Rooted 99.8942 96.137 3.7572
895 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Ranked 164 155.961 8.039
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared 23242.1 26955.1 3713
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Rooted 67.7394 71.4737 3.7343
exocyst complex component sec8. [swissprot;acc:q96a65] Divided 63.2983 67.1422 1.06073
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured 10247.8 11289 1.1016
leucyl-trna synthetase. [refseq;acc:nm_020117] Squared 21830.4 25308.2 1.15931
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Ranked 217.491 209.323 1.03902
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Measured Subtracted 5768.5 6342.05 573.55
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Ranked Divided 230.811 239.785 1.03888
lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared Subtracted 23242.1 26955.1 3713
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Divided 21830.4 25308.3 1.15931
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted Subtracted 73.8603 77.5904 3.7301
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 5167.88 4594.43 573.45
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 5208.27 5737.17 1.10155
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked Subtracted 243.34 235.322 8.018
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Rooted Divided 56.2142 59.6282 1.06073
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Ranked 272.878 283.472 1.03882
exocyst complex component sec15a. [swissprot;acc:q8tag9] Measured Subtracted 6201.54 6774.35 572.81
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared Divided 29924.3 34690.9 1.15929
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 5929.48 6531.48 1.10153
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Rooted 56.2142 59.6282 1.06073
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Subtracted 73.8553 77.585 3.7297
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Ranked 210.863 218.878 8.015
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Squared 23242.1 26955.1 3713
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked Divided 229.171 238.048 1.03874
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Measured 5929.55 6531.52 1.10152
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Rooted 56.2142 59.6282 1.06073
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Measured Subtracted 5859.25 6432.03 572.78
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Ranked 210.863 218.878 8.015
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Rooted 61.6325 65.3619 3.7294
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Squared Divided 21156.1 24524.1 1.1592
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Subtracted 23242.1 26955.1 3713
899 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 29345.7 34004.2 1.15875
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Rooted 66.5785 70.6139 1.06061
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Measured 5929.55 6531.52 1.10152
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 5859.25 6432.03 572.78
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Ranked 212.027 204.05 7.977
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Rooted 73.8426 77.5711 3.7285

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/