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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    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 Value Type Filtered red description Hugo green Interaction Map network_comparison Network Comparison Type
    Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
    Value Type  : Ranked
    Filtered  : 1
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Rank
    		red
    		description
    		Hugo
    		green
    		network_comparison
    501 238.704 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 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
    505 251.334 ad24 protein. [refseq;acc:nm_022451] NOC3L 234.672 1.071
    506 224.535 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] ING1 240.476
    507 251.299 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] WDR12 234.729 1.07059
    508 177.698 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 190.24 1.07058
    509 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 190.239 1.07057
    510 177.699 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 190.24
    511 250.053 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] NOL1 233.725 1.06986
    512 250.794 block of proliferation 1. [swissprot;acc:q14137] BOP1 234.433 1.06979
    513 218.596 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 204.344 1.06975
    514 218.613 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 204.382 1.06963
    515 251.297 pescadillo homolog 1. [swissprot;acc:o00541] PES1 234.941 1.06962
    516 228.255 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 213.422 1.0695
    517 219.537 metaxin 2. [swissprot;acc:o75431] MTX2 234.793 1.06949
    518 250.858 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] GNL3 234.563 1.06947
    519 218.702 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 204.582 1.06902
    520 214.754 sqv-7-like protein (fragment). [sptrembl;acc:o95454] SLC35D2 229.565 1.06897
    521 215.237 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] EXOSC4 230.07 1.06891
    522 222.893 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 208.523
    523 215.237 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] EXOSC2 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
    526 250.538 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] RRP1 234.401 1.06884
    527 248.56 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] DDX31 232.579 1.06871
    528 222.146 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] YME1L1 237.393 1.06864
    529 251.653 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] DDX18 235.506 1.06856
    530 227.483 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 212.994 1.06803
    531 223.356 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 209.149 1.06793
    532 250.942 zinc finger-like protein 9. [refseq;acc:nm_033414] ZNF622 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
    535 236.662 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] POLR2H 252.708 1.0678
    536 242.531 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB 227.136 1.06778
    537 229.803 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 215.301 1.06736
    538 237.627 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] POLR2L 253.604 1.06724
    539 236.964 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P 252.86 1.06708
    540 222.156 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 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
    545 248.866 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] EIF6 233.287 1.06678
    546 207.222 wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS 194.262 1.06671
    547 207.26 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK 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/