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 6691 to 6740 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1673 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Rooted 64.2279 66.3791 1.03349
    scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Squared 23713.7 26223.8 1.10585
    1674 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Measured 5791.14 6193.02 1.0694
    nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Squared 23713.7 26223.8 1.10585
    polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Rooted 62.9203 65.027 1.03348
    survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Ranked 228.496 231.729 1.01415
    1675 ammecr1 protein. [refseq;acc:nm_015365] Squared 23713.7 26223.8 1.10585
    probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] Ranked 228.496 231.729 1.01415
    retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Measured 5791.14 6193.02 1.0694
    similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Rooted 62.9203 65.027 1.03348
    1676 elongation factor 2 (ef-2). [swissprot;acc:p13639] 60.3002 62.3124 1.03337
    importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Ranked 218.691 215.645 1.01413
    indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Measured 5791.14 6193.02 1.0694
    mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Squared 23713.7 26223.8 1.10585
    1677 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Ranked 218.654 221.732 1.01408
    metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Rooted 60.3002 62.3124 1.03337
    nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Squared 17043.8 18846.2 1.10575
    ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Measured 6075.19 6496.61 1.06937
    1678 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 5763.25 6162.98 1.06936
    heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Squared 26940.8 29785.9 1.10561
    metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Rooted 60.3002 62.3124 1.03337
    serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Ranked 216.899 213.889 1.01407
    1679 gtp binding protein 2. [refseq;acc:nm_019096]
    mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Rooted 56.5094 58.3923 1.03332
    proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Measured 6180.24 6608.11 1.06923
    suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Squared 31163.9 34454.3 1.10558
    1680 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
    cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Ranked 216.899 213.889 1.01407
    methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Measured 6436.73 6882.16 1.0692
    skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Rooted 56.5094 58.3923 1.03332
    1681 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Ranked 216.899 213.889 1.01407
    f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Measured 6304.74 6740.66 1.06914
    glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Squared 31163.9 34454.3 1.10558
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Rooted 56.5094 58.3923 1.03332
    1682 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Measured 6304.74 6740.66 1.06914
    glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Squared 31163.9 34454.3 1.10558
    sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Ranked 216.899 213.889 1.01407
    tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Rooted 56.5094 58.3923 1.03332
    1683 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] Ranked 216.899 213.889 1.01407
    dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Squared 25120.7 27772.9 1.10558
    ring finger protein 20. [refseq;acc:nm_019592] Measured 5419.54 5793.94 1.06908
    sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Rooted 56.5094 58.3923 1.03332
    1684 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Squared 27060.6 29916.8 1.10555
    neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Rooted 56.5094 58.3923 1.03332
    ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Measured 5419.54 5793.94 1.06908
    sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Ranked 216.899 213.889 1.01407
    1685 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Squared 27060.6 29916.8 1.10555
    gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Measured 6088.07 6508.45 1.06905
    homeobox protein dlx-2. [swissprot;acc:q07687] Rooted 56.5094 58.3923 1.03332
    xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Ranked 216.899 213.889 1.01407

    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/