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 Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1025 to 1074 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    129 Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence LUC7L 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] Low confidence MAGEB4 1.0937 11285.3 10318.5
    Ranked 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] COL4A3BP 1.06609 220.969 235.572
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence VPS24 1.21277 94 114
    Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 1.50257 178263 118639
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence RRAGB 1.13764 56860.4 64686.5
    Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence NCBP2L 1.23044 54.2343 66.7323
    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] Low confidence NDUFS4 1.07372 62.9048 67.5424
    130 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] High confidence FOXP4 1.33287 2234.68 2978.53
    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 MAGED2 1.0937 11285.3 10318.5
    Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] High confidence CHMP4A 1.21277 94 114
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence ABRA 1.06602 225.495 211.529
    Squared 44050 protein. [refseq;acc:nm_178832] High confidence C10orf83 1.4861 148058 99628.4
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence RRAGA 1.136 56706.1 64418
    Rooted defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1 1.07337 69.1344 74.2065
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] High confidence no value 1.22626 55.1026 67.5701
    131 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 1.33285 2234.73 2978.57
    trophinin. [swissprot;acc:q12816] Low confidence TRO 1.0937 11285.3 10318.5
    Ranked 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] High confidence SON 1.21228 294.053 242.562
    striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence STRN4 1.065 213.878 200.825
    Squared helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577] NHLH2 1.13547 55864.7 49199.8
    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] High confidence PPP1R8 1.4861 148058 99628.4
    Rooted coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Low confidence F13A1 1.07324 63.8063 68.4797
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence no value 1.22577 55.1113 67.5537
    132 Measured 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 MAP2K4 1.09318 5948.88 5441.83
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence FOXP3 1.33253 2236.61 2980.35
    Ranked daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Low confidence DAZAP1 1.06411 220.268 206.997
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence TOB2 1.2069 350 290
    Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] ATG5 1.48606 36359.2 24466.8
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Low confidence HPRT1 1.13524 65137.2 73946.3
    Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence HAT1 1.22451 44.963 55.0576
    protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Low confidence TGM1 1.07324 63.8063 68.4797
    133 Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence GABARAP 1.33225 23421.5 17580.4
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence no value 1.09265 7013 7662.77
    Ranked prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] PROM1 1.06411 220.268 206.997
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence TOB1 1.2069 350 290
    Squared gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A 1.46039 1182.25 1726.55
    pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451] Low confidence BBS9 1.13517 55849.9 49199.6
    Rooted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] High confidence OSR1 1.22316 45.4558 55.5995
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence ABRA 1.07261 65.2217 69.9574
    134 Measured ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 1.09242 6670.21 7286.66
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence no value 1.32626 21785.2 16426.1
    Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP 1.2069 350 290
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Low confidence TAGLN 1.06391 218.561 205.431
    Squared helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] NHLH1 1.13494 55838.6 49199.4
    p66 alpha. [refseq;acc:nm_017660] High confidence GATAD2A 1.45434 81888.8 56306.5
    Rooted calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Low confidence CAPN1 1.07182 64.1512 68.7584
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] High confidence POLE4 1.2218 44.849 54.7964
    135 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 1.32626 21785.2 16426.1
    high-mobility group 20a. [refseq;acc:nm_018200] Low confidence HMG20A 1.09226 7248.24 7916.96

    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/