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 1012 to 1061 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
506 ING1 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Divided 224.535 240.476 1.071
507 EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Subtracted 215.237 230.07 14.833
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Divided 251.299 234.729 1.07059
508 CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 1.07058
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Subtracted 228.255 213.422 14.833
509 CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 177.698 190.239 1.07057
EXOSC3 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Subtracted 215.237 230.07 14.833
510 CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Divided 177.699 190.24 1.07057
EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Subtracted 215.237 230.07 14.833
511 NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Divided 250.053 233.725 1.06986
SLC35D2 sqv-7-like protein (fragment). [sptrembl;acc:o95454] Subtracted 214.754 229.565 14.811
512 BOP1 block of proliferation 1. [swissprot;acc:q14137] Divided 250.794 234.433 1.06979
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Subtracted 229.803 215.301 14.502
513 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 218.596 204.344 1.06975
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Subtracted 227.483 212.994 14.489
514 DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided 218.613 204.382 1.06963
PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Subtracted 222.893 208.523 14.37
515 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 14.368
PES1 pescadillo homolog 1. [swissprot;acc:o00541] Divided 251.297 234.941 1.06962
516 AKT3 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Subtracted 248.463 234.095 14.368
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Divided 228.255 213.422 1.0695
517 AKT2 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Subtracted 248.463 234.095 14.368
MTX2 metaxin 2. [swissprot;acc:o75431] Divided 219.537 234.793 1.06949
518 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 218.596 204.344 14.252
GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Divided 250.858 234.563 1.06947
519 DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted 218.613 204.382 14.231
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 218.702 204.582 1.06902
520 PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Subtracted 223.356 209.149 14.207
SLC35D2 sqv-7-like protein (fragment). [sptrembl;acc:o95454] Divided 214.754 229.565 1.06897
521 DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 218.702 204.582 14.12
EXOSC4 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Divided 215.237 230.07 1.06891
522 PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 222.893 208.523
SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Subtracted 229.709 215.631 14.078
523 EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Divided 215.237 230.07 1.06891
HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Subtracted 247.47 233.441 14.029
524 EXOSC3 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Divided 215.237 230.07 1.06891
HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Subtracted 247.47 233.441 14.029
525 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Divided 215.237 230.07 1.06891
526 no value histone h2b. [refseq;acc:nm_175055] Subtracted 247.47 233.441 14.029
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 250.538 234.401 1.06884
527 no value histone h2b.s (h2b/s). [swissprot;acc:p57053] Subtracted 247.47 233.441 14.029
DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Divided 248.56 232.579 1.06871
528 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] Subtracted 247.47 233.441 14.029
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Divided 222.146 237.393 1.06864
529 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Subtracted 247.47 233.441 14.029
530 HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Divided 227.483 212.994 1.06803
531 no value histone h2b.e (h2b/e). [swissprot;acc:q99879] Subtracted 247.47 233.441 14.029

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/