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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1025 to 1074 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    129 COL4A3BP 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] Low confidence 220.969 1.06609 235.572
    LUC7L Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence 4358.13 1.33348 5811.49
    MAGEB4 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 1.0937 10318.5
    NCBP2L Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 54.2343 1.23044 66.7323
    NDUFS4 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 62.9048 1.07372 67.5424
    PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] High confidence 178263 1.50257 118639
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 56860.4 1.13764 64686.5
    VPS24 Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 94 1.21277 114
    130 no value Rooted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 55.1026 1.22626 67.5701
    ABRA Ranked striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 225.495 1.06602 211.529
    C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] High confidence 148058 1.4861 99628.4
    CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 1.21277 114
    DAD1 Rooted defender against cell death 1 (dad-1). [swissprot;acc:p46966] Low confidence 69.1344 1.07337 74.2065
    FOXP4 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] High confidence 2234.68 1.33287 2978.53
    MAGED2 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 11285.3 1.0937 10318.5
    RRAGA Squared ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 56706.1 1.136 64418
    131 no value Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence 55.1113 1.22577 67.5537
    F13A1 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 63.8063 1.07324 68.4797
    FOXP1 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] High confidence 2234.73 1.33285 2978.57
    NHLH2 Squared helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577] Low confidence 55864.7 1.13547 49199.8
    PPP1R8 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 148058 1.4861 99628.4
    SON 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] 294.053 1.21228 242.562
    STRN4 striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 1.065 200.825
    TRO Measured trophinin. [swissprot;acc:q12816] 11285.3 1.0937 10318.5
    132 ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] High confidence 36359.2 1.48606 24466.8
    DAZAP1 Ranked daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Low confidence 220.268 1.06411 206.997
    FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence 2236.61 1.33253 2980.35
    HAT1 Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 44.963 1.22451 55.0576
    HPRT1 Squared hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Low confidence 65137.2 1.13524 73946.3
    MAP2K4 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] 5948.88 1.09318 5441.83
    TGM1 Rooted protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] 63.8063 1.07324 68.4797
    TOB2 Ranked tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 350 1.2069 290
    133 no value Measured ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 7013 1.09265 7662.77
    ABRA Rooted striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 65.2217 1.07261 69.9574
    BBS9 Squared pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451] 55849.9 1.13517 49199.6
    GABARAP Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 23421.5 1.33225 17580.4
    OSR1 Rooted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 45.4558 1.22316 55.5995
    PROM1 Ranked prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 220.268 1.06411 206.997
    TMEM132A Squared gbp protein isoform a. [refseq;acc:nm_017870] High confidence 1182.25 1.46039 1726.55
    TOB1 Ranked tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 350 1.2069 290
    134 no value Measured gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 1.32626 16426.1
    CAPN1 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 64.1512 1.07182 68.7584
    DAB2IP Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] High confidence 350 1.2069 290
    GATAD2A Squared p66 alpha. [refseq;acc:nm_017660] 81888.8 1.45434 56306.5
    GSTO2 Measured ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 6670.21 1.09242 7286.66
    NHLH1 Squared helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] 55838.6 1.13494 49199.4
    POLE4 Rooted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] High confidence 44.849 1.2218 54.7964
    TAGLN Ranked transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Low confidence 218.561 1.06391 205.431
    135 ATG3 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 21785.2 1.32626 16426.1
    CAPN2 Rooted calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Low confidence 64.1536 1.07181 68.7605

    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/