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 [...,...].
    Value Type Rank Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 908 to 957 of 29840 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Rank
    		description
    		Network Comparison Type
    		Filtered
    		red
    		green
    		network_comparison
    227 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Divided 0 424.258 369.011 1.14972
    228 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Subtracted 1225.08 1079.37 145.71
    myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 1 9035 7279.6 1.24114
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Subtracted 6417.81 7852.52 1434.71
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Divided 0 4089.65 4696.36 1.14835
    229 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 320.752 368.317 1.14829
    keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Subtracted 1225.08 1079.38 145.7
    myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 1 9035 7279.6 1.24114
    small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Subtracted 10434.4 11846.2 1411.8
    230 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 9649.61 11053.5 1403.89
    myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 9035 7279.6 1.24114
    star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Subtracted 0 1225.08 1079.38 145.7
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 1498.17 1718.6 1.14713
    231 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2017.91 1759.22 1.14705
    espin. [refseq;acc:nm_031475] Subtracted 1225.07 1079.38 145.69
    myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Divided 1 9035 7279.6 1.24114
    sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Subtracted 9649.61 11053.5 1403.89
    232 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 0 1663.73 1906.28 1.14579
    dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 1 9035 7279.6 1.24114
    hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Subtracted 0 2075.64 2220.68 145.04
    udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] 1 9649.61 11053.5 1403.89
    233 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 0 6158 6303 145
    maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Divided 348.823 399.534 1.14538
    myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 1 9035 7279.6 1.24114
    rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Subtracted 9649.61 11053.5 1403.89
    234 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 1224.65 1079.77 144.88
    map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 1 9649.61 11053.5 1403.89
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Divided 5181.2 6410.58 1.23728
    wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 0 5202.89 4550.64 1.14333
    235 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Subtracted 2113.27 2255.28 142.01
    integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Divided 1612.86 1843.92 1.14326
    neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted 1 9649.61 11053.5 1403.89
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 5181.2 6410.58 1.23728
    236 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Subtracted 0 1766.66 1908.13 141.47
    nitrogen fixation cluster-like. [refseq;acc:nm_014301] 1 9649.61 11053.5 1403.89
    peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Divided 0 2715.75 3103.01 1.1426
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 1 4723.53 5828.46 1.23392
    237 germ cell-less. [refseq;acc:nm_022471] Subtracted 0 1829.81 1694.05 135.76
    p28 ing5. [refseq;acc:nm_032329] Divided 2551.23 2243.69 1.13707
    star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Subtracted 1 9649.61 11053.5 1403.89
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided 4567.04 5631.2 1.23301
    238 casein kinase i alpha s-like. [refseq;acc:nm_145203] 0 2198.47 1933.94 1.13678
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 1 27642.5 22440.4 1.23182
    signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Subtracted 0 494.417 359.631 134.786
    star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 1 9649.61 11053.5 1403.89
    239 carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 7711.38 6265.8 1.23071
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 0 382.142 434.366 1.13666
    leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Subtracted 11170.7 11305 134.3
    neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 1 9649.61 11053.5 1403.89
    240 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Divided 7711.36 6265.79 1.23071

    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/