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 8586 to 8635 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    2147 seven in absentia homolog 2. [refseq;acc:nm_005067] Rooted 59.6479 61.0522 1.02354
    tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Measured 5859.1 6173.7 1.05369
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Squared 26623 28920.4 1.08629
    2148 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Ranked 217.871 219.366 1.00686
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Rooted 59.8865 61.296 1.02354
    deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Measured 4644.58 4892.06 1.05328
    step ii splicing factor slu7. [refseq;acc:nm_006425] Squared 26623 28920.4 1.08629
    2149 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Ranked 217.871 219.366 1.00686
    bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Rooted 59.8891 61.2986 1.02354
    importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Measured 5778.62 6086.03 1.0532
    lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Squared 25625 27835.7 1.08627
    2150 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Ranked 217.871 219.366 1.00686
    karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Measured 5779.82 6086.64 1.05308
    lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] Squared 25625 27835.7 1.08627
    testis-specific bromodomain protein. [refseq;acc:nm_001726] Rooted 59.8895 61.2991 1.02354
    2151 apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Ranked 217.871 219.366 1.00686
    early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Measured 4871.11 5129.63 1.05307
    nag14 protein. [refseq;acc:nm_022143] Rooted 59.8891 61.2986 1.02354
    tripartite motif protein 2. [swissprot;acc:q9c040] Squared 44886.6 41323.6 1.08622
    2152 40s ribosomal protein s23. [swissprot;acc:p39028] Measured 3560.63 3381.34 1.05302
    bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] Rooted 59.8886 61.2981 1.02354
    dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Squared 18838.9 20460.9 1.0861
    vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Ranked 200.063 198.71 1.00681
    2153 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Measured 3560.63 3381.34 1.05302
    hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Squared 26102.8 28346.1 1.08594
    mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Rooted 66.176 67.7325 1.02352
    vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Ranked 200.063 198.71 1.00681
    2154 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Measured 6884.69 7247.36 1.05268
    dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Rooted 64.9289 66.456 1.02352
    sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Squared 24415.7 26511.8 1.08585
    vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Ranked 200.063 198.71 1.00681
    2155 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Rooted 59.2785 60.6708 1.02349
    cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Ranked 200.063 198.71 1.00681
    centaurin gamma 2. [swissprot;acc:q9upq3] Measured 5701.81 6000.03 1.0523
    traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Squared 27139.5 29466.5 1.08574
    2156 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Ranked 200.063 198.71 1.00681
    general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Measured 5701.81 6000.03 1.0523
    peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Rooted 59.2785 60.6708 1.02349
    ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Squared 40276.1 37105 1.08546
    2157 centaurin gamma 1. [swissprot;acc:q99490] Measured 5701.81 6000.03 1.0523
    iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Rooted 59.2785 60.6708 1.02349
    ubiquitin. [swissprot;acc:p02248] Squared 29644.9 32177.9 1.08544
    vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Ranked 200.063 198.71 1.00681
    2158 centaurin gamma 3. [swissprot;acc:q96p47] Measured 5701.81 6000.03 1.0523
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Ranked 206.401 207.796 1.00676
    proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Squared 29343.2 31849.8 1.08542
    shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Rooted 59.3962 58.0334 1.02348
    2159 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Ranked 215.921 214.474 1.00675
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Squared 18185.9 19737.1 1.0853
    serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Measured 5379.49 5660.18 1.05218

    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/