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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 238.704 255.68 1.07112
502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] ARHGAP26
503 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] RGN
504 oligophrenin 1. [swissprot;acc:o60890] OPHN1
505 ad24 protein. [refseq;acc:nm_022451] NOC3L 251.334 234.672 1.071
506 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] ING1 224.535 240.476
507 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] WDR12 251.299 234.729 1.07059
508 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 177.698 190.24 1.07058
509 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 190.239 1.07057
510 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 177.699 190.24
511 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] NOL1 250.053 233.725 1.06986
512 block of proliferation 1. [swissprot;acc:q14137] BOP1 250.794 234.433 1.06979
513 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 218.596 204.344 1.06975
514 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 218.613 204.382 1.06963
515 pescadillo homolog 1. [swissprot;acc:o00541] PES1 251.297 234.941 1.06962
516 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 228.255 213.422 1.0695
517 metaxin 2. [swissprot;acc:o75431] MTX2 219.537 234.793 1.06949
518 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] GNL3 250.858 234.563 1.06947
519 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 218.702 204.582 1.06902
520 sqv-7-like protein (fragment). [sptrembl;acc:o95454] SLC35D2 214.754 229.565 1.06897
521 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] EXOSC4 215.237 230.07 1.06891
522 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 222.893 208.523
523 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] EXOSC2 215.237 230.07
524 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] EXOSC3
525 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] EXOSC5
526 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] RRP1 250.538 234.401 1.06884
527 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] DDX31 248.56 232.579 1.06871
528 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] YME1L1 222.146 237.393 1.06864
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] DDX18 251.653 235.506 1.06856
530 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 227.483 212.994 1.06803
531 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 223.356 209.149 1.06793
532 zinc finger-like protein 9. [refseq;acc:nm_033414] ZNF622 250.942 235.004 1.06782
533 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] SLC45A2
534 guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] no value
535 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] POLR2H 236.662 252.708 1.0678
536 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB 242.531 227.136 1.06778
537 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 229.803 215.301 1.06736
538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] POLR2L 237.627 253.604 1.06724
539 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P 236.964 252.86 1.06708
540 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 222.156 208.201 1.06703
541 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2
542 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B
543 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1
544 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A
545 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] EIF6 248.866 233.287 1.06678
546 wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS 207.222 194.262 1.06671
547 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK 207.26 194.346 1.06645
548 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2
549 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value
550 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK

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/