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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 432 to 481 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    108 SLC39A6 Subtracted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] High confidence 209.299 39.888 249.187
    109 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Low confidence 197.762 14.251 212.013
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence 209.299 39.888 249.187
    GNB4 Divided guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 1.24856 333.281
    NEURL neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 1.07239 216.996
    110 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 197.752 1.07221 212.031
    CREG2 Subtracted cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 197.763 14.248 212.011
    DTX2 Divided deltex 2. [refseq;acc:nm_020892] High confidence 333.144 1.2459 267.393
    NAPG Subtracted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 39.888 249.187
    111 DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Low confidence 197.779 14.204 211.983
    DTX1 Divided deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 332.925 1.24563 267.274
    GAD1 Subtracted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 39.888 249.187
    VPS33A Divided vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 203.914 1.07217 190.189
    112 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 197.762 1.07206 212.013
    DLGAP4 Subtracted disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 197.779 14.204 211.983
    PBK Divided t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] High confidence 332.874 1.24557 267.246
    POLE4 Subtracted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 275.754 39.846 235.908
    113 CREG2 Divided cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Low confidence 197.763 1.07205 212.011
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 1.24557 267.246
    PPP2CA Subtracted serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 194.372 39.832 234.204
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 14.197 210.566
    114 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] High confidence 229.818 37.447 267.265
    DLGAP1 Divided disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Low confidence 197.779 1.07182 211.983
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 1.24557 267.246
    MRPS17 Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 58 14 44
    115 DLGAP4 Divided disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 197.779 1.07182 211.983
    HAT1 Subtracted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence 277.546 37.085 240.461
    KHDRBS2 Divided kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 332.874 1.24557 267.246
    SLC25A43 Subtracted mitochondrial solute carrier protein. [refseq;acc:nm_145305] Low confidence 58 14 44
    116 no value testican-3 precursor. [swissprot;acc:q9bq16] 220.395 13.994 234.389
    GNB3 Divided guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] High confidence 268.565 1.24545 334.483
    HMG20B Subtracted high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 208.52 36.925 171.595
    VPS18 Divided vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 204.161 1.07008 190.791
    117 ABRA Subtracted striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 225.495 13.966 211.529
    F13A1 Divided coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 1.06935 211.713
    HMG20A Subtracted high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 36.81 171.778
    NEURL Divided neuralized-like. [refseq;acc:nm_004210] 332.326 1.24491 266.948
    118 NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 284.753 1.24382 228.934
    OSR1 Subtracted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 36.237 237.79
    SPOCK1 testican-1 precursor (spock protein). [swissprot;acc:q08629] Low confidence 220.254 13.857 234.111
    TGM1 Divided protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] 226.395 1.06935 211.713
    119 ADIPOR2 Subtracted adiponectin receptor 2. [refseq;acc:nm_024551] High confidence 281.582 35.211 246.371
    NDUFS4 Divided 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] 318.982 1.23157 259.004
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 225.666 1.06897 211.107
    SPOCK2 Subtracted testican-2 precursor. [swissprot;acc:q92563] 220.222 13.825 234.047
    120 no value nanos (fragment). [sptrembl;acc:q8wy41] 203.66 13.819 217.479
    DVL1 Divided segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 203.016 1.0687 189.965
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 269.278 1.21699 327.709
    TIA1 Subtracted nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 34.484 192.715
    121 CTH Divided cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 1.2169 327.655

    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/