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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 430 to 479 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    108 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] DLGAP3 Divided Low confidence 197.731 212.069 1.07251
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 High confidence 252.296 201.995 1.24902
    liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 Subtracted 209.299 249.187 39.888
    109 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] CREG1 Low confidence 197.762 212.013 14.251
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] GAD2 High confidence 209.299 249.187 39.888
    guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 Divided 266.933 333.281 1.24856
    neuralized-like. [refseq;acc:nm_004210] NEURL Low confidence 232.704 216.996 1.07239
    110 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] CREG2 Subtracted 197.763 212.011 14.248
    deltex 2. [refseq;acc:nm_020892] DTX2 Divided High confidence 333.144 267.393 1.2459
    disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] no value Low confidence 197.752 212.031 1.07221
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG Subtracted High confidence 209.299 249.187 39.888
    111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 Divided 332.925 267.274 1.24563
    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] DLGAP1 Subtracted Low confidence 197.779 211.983 14.204
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 High confidence 209.299 249.187 39.888
    vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A Divided Low confidence 203.914 190.189 1.07217
    112 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] CREG1 197.762 212.013 1.07206
    disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] DLGAP4 Subtracted 197.779 211.983 14.204
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 High confidence 275.754 235.908 39.846
    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] PBK Divided 332.874 267.246 1.24557
    113 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] CREG2 Low confidence 197.763 212.011 1.07205
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 High confidence 332.874 267.246 1.24557
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 Subtracted Low confidence 224.763 210.566 14.197
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA High confidence 194.372 234.204 39.832
    114 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Low confidence 58 44 14
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 High confidence 229.818 267.265 37.447
    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] DLGAP1 Divided Low confidence 197.779 211.983 1.07182
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 High confidence 332.874 267.246 1.24557
    115 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] DLGAP4 Low confidence 197.779 211.983 1.07182
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Subtracted High confidence 277.546 240.461 37.085
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Divided 332.874 267.246 1.24557
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] SLC25A43 Subtracted Low confidence 58 44 14
    116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] GNB3 Divided High confidence 268.565 334.483 1.24545
    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] HMG20B Subtracted 208.52 171.595 36.925
    testican-3 precursor. [swissprot;acc:q9bq16] no value Low confidence 220.395 234.389 13.994
    vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] VPS18 Divided 204.161 190.791 1.07008
    117 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] F13A1 226.395 211.713 1.06935
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A Subtracted High confidence 208.588 171.778 36.81
    neuralized-like. [refseq;acc:nm_004210] NEURL Divided 332.326 266.948 1.24491
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] ABRA Subtracted Low confidence 225.495 211.529 13.966
    118 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] NDUFA12 Divided High confidence 284.753 228.934 1.24382
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Subtracted 274.027 237.79 36.237
    protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] TGM1 Divided Low confidence 226.395 211.713 1.06935
    testican-1 precursor (spock protein). [swissprot;acc:q08629] SPOCK1 Subtracted 220.254 234.111 13.857
    119 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 High confidence 281.582 246.371 35.211
    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] NDUFS4 Divided 318.982 259.004 1.23157
    natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] SLC11A1 Low confidence 225.666 211.107 1.06897
    testican-2 precursor. [swissprot;acc:q92563] SPOCK2 Subtracted 220.222 234.047 13.825
    120 nanos (fragment). [sptrembl;acc:q8wy41] no value 203.66 217.479 13.819
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 High confidence 227.199 192.715 34.484
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Divided 269.278 327.709 1.21699

    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/