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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2008 to 2057 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    502 RRM1 Measured ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 6913.6 7907.05 1.1437
    503 no value Rooted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 177.987 194.29 1.0916
    RGN Ranked senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 238.704 255.68 1.07112
    TP53BP2 Measured tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 15182.5 13277.9 1.14344
    TULP3 Squared tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 30286.5 36362 1.2006
    504 ECHS1 Measured enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 10067.9 11511 1.14334
    OPHN1 Ranked oligophrenin 1. [swissprot;acc:o60890] 238.704 255.68 1.07112
    RRAGA Rooted ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 144.606 157.824 1.09141
    VPS35 Squared vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 30286.5 36362 1.2006
    505 CBLB Measured signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 6856.71 7838.3 1.14316
    NOC3L Ranked ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 1.071
    PRKCZ Squared protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 30286.5 36362 1.2006
    RRAGC Rooted ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 144.606 157.824 1.09141
    506 EIF6 Measured eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 3893.85 4450.98 1.14308
    ING1 Ranked inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 224.535 240.476 1.071
    RRAGB Rooted ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 144.606 157.824 1.09141
    VAV2 Squared vav-2 protein. [swissprot;acc:p52735] 31377.3 37670.1 1.20055
    507 ANLN Rooted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 144.606 157.824 1.09141
    CBL Measured cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 6875.08 7858.38 1.14302
    NPEPPS Squared puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 23512.2 28206.2 1.19964
    WDR12 Ranked wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 251.299 234.729 1.07059
    508 AGPAT2 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 7556.75 8636.87 1.14293
    CPA3 Ranked mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 1.07058
    GNL2 Rooted autoantigen ngp-1. [swissprot;acc:q13823] 49.4756 53.9896 1.09124
    LTA4H Squared leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 23512.2 28206.2 1.19964
    509 no value Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 7551.8 8630.06 1.14278
    CPA6 Ranked carboxypeptidase b precursor. [refseq;acc:nm_020361] 177.698 190.239 1.07057
    DHODH Squared dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 23512.2 28206.2 1.19964
    MRPL11 Rooted 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 50.2583 46.057 1.09122
    510 BRF1 Squared transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 17281.7 20723 1.19913
    CPB2 Ranked plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 177.699 190.24 1.07057
    GRB2 Measured growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 5975.11 6826.24 1.14245
    PPP1R7 Rooted protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 149.397 136.972 1.09071
    511 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 50.5979 46.392 1.09066
    NEK2 Measured serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 5975.11 6826.24 1.14245
    NOL1 Ranked proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 250.053 233.725 1.06986
    NOLA1 Squared nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 17281.7 20723 1.19913
    512 no value Measured small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 10807.4 12338.5 1.14167
    BOP1 Ranked block of proliferation 1. [swissprot;acc:q14137] 250.794 234.433 1.06979
    CBS Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 19987.6 23960.7 1.19878
    PPM1B Rooted protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 56.3798 61.4858 1.09056
    513 AGPAT3 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1.14143
    DVL1 Ranked segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 218.596 204.344 1.06975
    RHOC Squared transforming protein rhoc (h9). [swissprot;acc:p08134] 19987.6 23960.7 1.19878
    RPL4 Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
    514 AGPAT4 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 7477 8532.02 1.1411
    DVL2 Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 218.613 204.382 1.06963
    TST Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 1.19878
    XAB2 Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
    515 no value Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 1.14099

    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/