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 2130 to 2179 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1065 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Divided 6393.81 6984.94 1.09245
1066 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 5732.73 6256.63 523.9
leucyl-trna synthetase. [refseq;acc:nm_020117] Divided 5417.06 5917.79 1.09244
1067 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 5417.07 1.09243
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 5732.73 6256.63 523.9
1068 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 5857.48 6380.4 522.92
exocyst complex component sec15a. [swissprot;acc:q8tag9] Divided 6201.54 6774.35 1.09237
1069 elongation factor 2 (ef-2). [swissprot;acc:p13639] 5494.73 6001.08 1.09215
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Subtracted 6251.32 6774.12 522.8
1070 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Divided 5494.73 6001.08 1.09215
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 6042.31 6565.03 522.72
1071 40s ribosomal protein s30. [swissprot;acc:q05472] 5893.97 6416.07 522.1
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 5494.73 6001.08 1.09215
1072 electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Subtracted 7794.41 8316.04 521.63
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Divided 5207.39 5687.2 1.09214
1073 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Subtracted 5364.3 5885.48 521.18
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Divided 5207.39 5687.2 1.09214
1074 putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Subtracted 5364.3 5885.48 521.18
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Divided 5207.39 5687.2 1.09214
1075 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Subtracted 4359.82 4880.99 521.17
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Divided 6441.56 7034.86 1.09211
1076 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Subtracted 4565.34 5085.92 520.58
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Divided 6439.63 7032.19 1.09202
1077 myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Subtracted 4565.34 5085.92 520.58
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Divided 6439.66 7032.22 1.09202
1078 myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Subtracted 4565.34 5085.92 520.58
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Divided 6439.63 7032.19 1.09202
1079 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Subtracted 4565.34 5085.92 520.58
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Divided 6439.66 7032.22 1.09202
1080 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Subtracted 4565.34 5085.92 520.58
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Divided 6439.3 7031.73 1.092
1081 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Subtracted 4565.34 5085.92 520.58
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Divided 6439.3 7031.73 1.092
1082 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] Subtracted 5364.77 5884.89 520.12
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Divided 6439.35 7031.8 1.092
1083 exocyst complex component sec15b. [swissprot;acc:q9y2d4] 6213.51 6785.04 1.09198
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Subtracted 5511.96 6031.95 519.99
1084 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 7444.28 7964 519.72
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Divided 6437.49 7029.22 1.09192
1085 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 6520.28 7119.28 1.09187
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Subtracted 6343.26 6862.94 519.68
1086 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] 5365.06 5884.52 519.46
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Divided 6520.28 7119.28 1.09187
1087 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 5732.73 6256.63 1.09139
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Subtracted 6439.79 6959.21 519.42
1088 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
tax interaction protein 1. [refseq;acc:nm_014604] Divided 5732.73 6256.63 1.09139
1089 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Subtracted 6439.79 6959.21 519.42
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Divided 6390.28 6973.08 1.0912
1090 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Subtracted 6439.79 6959.21 519.42

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/