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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2877 to 2926 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1439 FADS3 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Divided 225.039 229.573 1.02015
UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted 166.846 170.989 4.143
1440 OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 224.159 220.017 4.142
SMAD4 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Divided 225.039 229.573 1.02015
1441 FADS2 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]
GPI 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] Subtracted 217.704 221.839 4.135
1442 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided 225.039 229.573 1.02015
RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Subtracted 218.591 214.457 4.134
1443 GLUD2 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Divided 203.908 207.998 1.02006
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 172.543 168.417 4.126
1444 CPSF6 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 218.664 214.55 4.114
GLUDP5 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Divided 203.908 207.998 1.02006
1445 PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 134.233 136.922 1.02003
XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Subtracted 224.476 220.363 4.113
1446 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 4.098
HSPB1 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] Divided 221.817 226.23 1.01989
1447 DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Subtracted 224.509 220.411 4.098
POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Divided 250.854 255.842 1.01988
1448 RTN4 reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Subtracted 207.038 211.13 4.092
ZMPSTE24 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Divided 226.532 222.117 1.01988
1449 GLUD2 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Subtracted 203.908 207.998 4.09
TNPO3 transportin-sr; importin 12. [refseq;acc:nm_012470] Divided 225.305 229.766 1.0198
1450 GLUDP5 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Subtracted 203.908 207.998 4.09
HSPB8 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] Divided 221.804 226.194 1.01979
1451 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 1.01978
SAP18 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Subtracted 207.024 211.089 4.065
1452 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Divided 160.381 163.554 1.01978
DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Subtracted 212.001 207.937 4.064
1453 EHD4 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 207.024 211.086 4.062
RTN4 reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Divided 207.038 211.13 1.01976
1454 ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Subtracted 240.077 236.015 4.062
SAP18 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Divided 207.024 211.089 1.01964
1455 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 1.01962
EHD2 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Subtracted 211.086 4.062
1456 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3]
EHD4 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Divided 1.01962
1457 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Subtracted 215.328 211.267 4.061
EHD2 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Divided 207.024 211.086 1.01962
1458 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Subtracted 211.085 4.061
EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3] Divided 211.086 1.01962
1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 188.637 1.01961
RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Subtracted 207.019 211.077 4.058
1460 SFRS10 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 211.066 4.056
TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Divided 205.817 209.851 1.0196
1461 MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Subtracted 171.231 167.177 4.054
RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Divided 207.019 211.077 1.0196
1462 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 205.817 209.851
SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Subtracted 171.231 167.177 4.054
1463 no value pnas-18. [sptrembl;acc:q9bzu3] Divided 161.056 164.211 1.01959
DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Subtracted 171.231 167.177 4.054

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
- Hugo is the HGNC identifier if it exists
- 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/