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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2875 to 2924 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
red
green
network_comparison
1438 PGGT1B Divided geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 225.039 229.573 1.02015
UBE2E1 Subtracted ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] 166.846 170.989 4.143
1439 FADS3 Divided fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] 225.039 229.573 1.02015
UBE2E4P Subtracted ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 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 Divided mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] 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 Subtracted 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] 217.704 221.839 4.135
1442 no value Divided fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 225.039 229.573 1.02015
RANBP6 Subtracted ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 218.591 214.457 4.134
1443 GLUD2 Divided glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 203.908 207.998 1.02006
PYCR1 Subtracted pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 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 Divided glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] 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 Subtracted exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 224.476 220.363 4.113
1446 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 4.098
HSPB1 Divided 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] 221.817 226.23 1.01989
1447 DCP1A Subtracted transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 224.509 220.411 4.098
POLE3 Divided dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 250.854 255.842 1.01988
1448 RTN4 Subtracted 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] 207.038 211.13 4.092
ZMPSTE24 Divided 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] 226.532 222.117 1.01988
1449 GLUD2 Subtracted glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 203.908 207.998 4.09
TNPO3 Divided transportin-sr; importin 12. [refseq;acc:nm_012470] 225.305 229.766 1.0198
1450 GLUDP5 Subtracted glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] 203.908 207.998 4.09
HSPB8 Divided alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 221.804 226.194 1.01979
1451 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 1.01978
SAP18 Subtracted sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] 207.024 211.089 4.065
1452 no value Divided cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 160.381 163.554 1.01978
DRAP1 Subtracted dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 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 Divided 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] 207.038 211.13 1.01976
1454 ATG5 Subtracted autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 240.077 236.015 4.062
SAP18 Divided sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] 207.024 211.089 1.01964
1455 EHD1 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 1.01962
EHD2 Subtracted eh-domain containing protein 2. [swissprot;acc:q9nzn4] 211.086 4.062
1456 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3]
EHD4 Divided eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 1.01962
1457 no value Subtracted transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 211.267 4.061
EHD2 Divided eh-domain containing protein 2. [swissprot;acc:q9nzn4] 207.024 211.086 1.01962
1458 EHD1 Subtracted eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 4.061
EHD3 Divided eh-domain containing protein 3. [swissprot;acc:q9nzn3] 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 Subtracted reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 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 Divided thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 209.851 1.0196
1461 MAPK11 Subtracted 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] 171.231 167.177 4.054
RTN1 Divided reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 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 Subtracted sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 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/