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 501 to 550 of 9634 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Rank
    		description
    		Interaction Map
    		Filtered
    		red
    		green
    		network_comparison
    126 calcyphosine. [swissprot;acc:q13938] High confidence 0 472.524 635.875 1.3457
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 24250 18164.9 1.33499
    fos-related antigen 2. [swissprot;acc:p15408] Low confidence 0 3205.98 2407.27 1.33179
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 1 11285.3 10318.5 1.0937
    127 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] High confidence 0 86 64 1.34375
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Low confidence 1 11285.3 10318.5 1.0937
    transcription factor jun-d. [swissprot;acc:p17535] High confidence 5638.2 7523.39 1.33436
    ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [swissprot;acc:q9udw1] Low confidence 0 680.5 511.5 1.3304
    128 double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563] 294 391 1.32993
    luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 1 4355.61 5810.82 1.3341
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 11285.3 10318.5 1.0937
    mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] High confidence 0 81.504 60.8613 1.33918
    129 amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [swissprot;acc:p51172] Low confidence 146.219 194.326 1.32901
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence 1 4358.13 5811.49 1.33348
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 11285.3 10318.5 1.0937
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] High confidence 0 606.485 454.837 1.33341
    130 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1 2234.68 2978.53 1.33287
    maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0 42 56 1.33333
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Low confidence 1 11285.3 10318.5 1.0937
    phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 0 707.801 937.501 1.32453
    131 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 645.504 851.77 1.31954
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] High confidence 1 2234.73 2978.57 1.33285
    serpin b11. [swissprot;acc:q96p15] 0 42 56 1.33333
    trophinin. [swissprot;acc:q12816] Low confidence 1 11285.3 10318.5 1.0937
    132 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] High confidence 0 42 56 1.33333
    dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Low confidence 1 5948.88 5441.83 1.09318
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence 2236.61 2980.35 1.33253
    wd-repeat protein 5 (wd-repeat protein big-3). [swissprot;acc:q9ugp9] Low confidence 0 251.947 191.971 1.31242
    133 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] High confidence 252 335 1.32937
    cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035] Low confidence 874 1139 1.3032
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 1 23421.5 17580.4 1.33225
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 7013 7662.77 1.09265
    134 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 6670.21 7286.66 1.09242
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 21785.2 16426.1 1.32626
    mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 260.986 346.751 1.32862
    presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Low confidence 874 1139 1.3032
    135 apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 1 21785.2 16426.1 1.32626
    high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 7248.24 7916.96 1.09226
    maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 0 265.513 203.832 1.30261
    rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] High confidence 814.485 613.614 1.32736
    136 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Low confidence 200.834 154.324 1.30138
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] High confidence 1 3620.77 4763.34 1.31556
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 7020.48 7667.34 1.09214
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] High confidence 0 1526.38 1150.51 1.3267
    137 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Low confidence 200.759 154.279 1.30127
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] High confidence 1 3620.77 4763.34 1.31556
    heat shock factor binding protein 1. [swissprot;acc:o75506] 0 1631.18 1233.41 1.3225
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 1 6139.6 6699.58 1.09121
    138 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 0 200.759 154.279 1.30127
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1 6709 7313.38 1.09008

    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/