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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2430 to 2479 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    608 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared 24560.6 29071.1 1.18365
    nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Measured 4510.61 5098.74 1.13039
    splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Rooted 59.6517 64.4642 1.08068
    609 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Measured 3886.62 3438.82 1.13022
    histone h2b.s (h2b/s). [swissprot;acc:p57053] Ranked 247.47 233.441 1.0601
    pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted 62.9281 67.99 1.08044
    pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Squared 12276.9 14526 1.1832
    610 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Rooted 136.706 126.565 1.08012
    histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked 247.47 233.441 1.0601
    kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1.12907
    pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Squared 12347.6 14594.8 1.18199
    611 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 23487.1 27726.3 1.18049
    dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured 5148.71 5811.74 1.12878
    histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked 247.47 233.441 1.0601
    upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted 51.0091 55.0909 1.08002
    612 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Measured 3975.77 4485.05 1.1281
    l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Rooted 57.1949 61.7633 1.07987
    testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Ranked 247.47 233.441 1.0601
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Squared 18595.6 21936.3 1.17965
    613 histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked 247.47 233.441 1.0601
    n-myc proto-oncogene protein. [swissprot;acc:p04198] Rooted 57.1971 61.7626 1.07982
    n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Squared 17550.2 20701.1 1.17954
    trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 3975.77 4485.05 1.1281
    614 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Squared 51527.6 43689.1 1.17942
    ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 1.07973
    homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Ranked 214.257 202.125 1.06002
    solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Measured 11222.2 9948.93 1.12798
    615 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Squared 51527.6 43689.1 1.17942
    cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured 11222.2 9948.93 1.12798
    ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Rooted 57.2007 61.7615 1.07973
    homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Ranked 214.257 202.132 1.05999
    616 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Measured 11222.2 9948.93 1.12798
    coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Squared 51527.6 43689.1 1.17942
    homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Ranked 214.257 202.132 1.05999
    nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted 57.2007 61.7615 1.07973
    617 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared 51527.6 43689.1 1.17942
    dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Measured 5162.52 5822.47 1.12783
    elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Rooted 57.2008 61.7614 1.07973
    homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Ranked 214.257 202.135 1.05997
    618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
    myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted 57.208 61.7592 1.07956
    nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured 7878.27 8879.08 1.12703
    peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 1.17942
    619 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
    dendritic cell protein. [refseq;acc:nm_006360] Rooted 63.847 68.8873 1.07894
    forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Ranked 214.256 202.139 1.05994
    nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Measured 3879.99 4371.24 1.12661
    620 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
    gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Ranked 214.256 202.14 1.05994
    homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared 32208.8 37986.6 1.17939

    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
    - 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/