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 [...,...].
    Network Comparison Type Rank Gene description Value Type Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1025 to 1074 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    129 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted NCBP2L High confidence 1.23044 54.2343 66.7323
    goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Ranked COL4A3BP Low confidence 1.06609 220.969 235.572
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured LUC7L High confidence 1.33348 4358.13 5811.49
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Low confidence 1.0937 11285.3 10318.5
    nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted NDUFS4 1.07372 62.9048 67.5424
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked VPS24 High confidence 1.21277 94 114
    pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared PCF11 1.50257 178263 118639
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Low confidence 1.13764 56860.4 64686.5
    130 44050 protein. [refseq;acc:nm_178832] C10orf83 High confidence 1.4861 148058 99628.4
    defender against cell death 1 (dad-1). [swissprot;acc:p46966] Rooted DAD1 Low confidence 1.07337 69.1344 74.2065
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured FOXP4 High confidence 1.33287 2234.68 2978.53
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted no value 1.22626 55.1026 67.5701
    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] Measured MAGED2 Low confidence 1.0937 11285.3 10318.5
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked CHMP4A High confidence 1.21277 94 114
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared RRAGA Low confidence 1.136 56706.1 64418
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Ranked ABRA 1.06602 225.495 211.529
    131 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Rooted F13A1 1.07324 63.8063 68.4797
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured FOXP1 High confidence 1.33285 2234.73 2978.57
    helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577] Squared NHLH2 Low confidence 1.13547 55864.7 49199.8
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted no value High confidence 1.22577 55.1113 67.5537
    nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Squared PPP1R8 1.4861 148058 99628.4
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked SON 1.21228 294.053 242.562
    striatin 4 (zinedin). [swissprot;acc:q9nrl3] STRN4 Low confidence 1.065 213.878 200.825
    trophinin. [swissprot;acc:q12816] Measured TRO 1.0937 11285.3 10318.5
    132 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared ATG5 High confidence 1.48606 36359.2 24466.8
    daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked DAZAP1 Low confidence 1.06411 220.268 206.997
    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] Measured MAP2K4 1.09318 5948.88 5441.83
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 High confidence 1.33253 2236.61 2980.35
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted HAT1 1.22451 44.963 55.0576
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared HPRT1 Low confidence 1.13524 65137.2 73946.3
    protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Rooted TGM1 1.07324 63.8063 68.4797
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked TOB2 High confidence 1.2069 350 290
    133 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured GABARAP 1.33225 23421.5 17580.4
    gbp protein isoform a. [refseq;acc:nm_017870] Squared TMEM132A 1.46039 1182.25 1726.55
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted OSR1 1.22316 45.4558 55.5995
    prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Ranked PROM1 Low confidence 1.06411 220.268 206.997
    pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451] Squared BBS9 1.13517 55849.9 49199.6
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured no value 1.09265 7013 7662.77
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Rooted ABRA 1.07261 65.2217 69.9574
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked TOB1 High confidence 1.2069 350 290
    134 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Measured GSTO2 Low confidence 1.09242 6670.21 7286.66
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted CAPN1 1.07182 64.1512 68.7584
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked DAB2IP High confidence 1.2069 350 290
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted POLE4 1.2218 44.849 54.7964
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured no value 1.32626 21785.2 16426.1
    helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] Squared NHLH1 Low confidence 1.13494 55838.6 49199.4
    p66 alpha. [refseq;acc:nm_017660] GATAD2A High confidence 1.45434 81888.8 56306.5
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Ranked TAGLN Low confidence 1.06391 218.561 205.431
    135 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted NCBP2 High confidence 1.21253 54.935 66.6101
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured ATG3 1.32626 21785.2 16426.1

    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
    - Hugo is the HGNC identifier if it exists
    - 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/