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 Network Comparison Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 530 to 579 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    67 ATG4B Squared Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 144876 81136.5 63739.5
    GBE1 Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 47.2654 16.6032
    GNAT2 Ranked Divided guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 336.075 1.25805
    MAGEA8 Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 219048 129762 1.68808
    MYO15A Rooted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 63.8686 47.2654 1.35128
    PPP2R2B Ranked Subtracted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 187.458 243.677 56.219
    RAF1 Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 14007.3 3749.2
    68 ARRB1 Divided beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 1.59177
    CCNG2 Subtracted cyclin g2. [swissprot;acc:q16589] 17738.6 13995.7 3742.9
    GABARAP Squared gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 139741 78454.6 61286.4
    GNAZ Ranked Divided guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 336.075 1.25805
    MAGEC1 Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 219048 129762 1.68808
    PPP2R2C Ranked Subtracted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 187.462 243.673 56.211
    PYGB Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 47.2654 16.6032
    PYGM Divided glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1.35128
    69 CCNG1 Measured Subtracted cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 13995.6 3742.9
    GNAT1 Ranked Divided guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 336.075 1.25805
    MAGEA4 Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 129762 1.68808
    NDUFA12 Ranked Subtracted 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] 284.753 228.934 55.819
    NEUROD2 Rooted Divided neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 27.9136 37.2872 1.33581
    PCF11 Squared Subtracted pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 118639 59624
    PYGL Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 47.2654 16.6032
    SPATA6 Measured Divided spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 10307.5 1.59177
    70 no value Squared melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 219048 129762 1.68808
    Subtracted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 129597 73157.5 56439.5
    AMPD2 Measured Divided amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 1.59177
    CHD3 Rooted chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 27.9136 37.2872 1.33581
    GNAI2 Ranked guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 267.142 336.074 1.25804
    MYO15A Rooted Subtracted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 63.8686 47.2654 16.6032
    PPP2R1B Ranked serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 188.688 242.742 54.054
    PPP2R5E Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 17738.5 13995.7 3742.8
    71 no value Divided serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 4556.78 2945.26 1.54716
    ATG3 Squared Subtracted apg3p; pc3-96 protein. [refseq;acc:nm_022488] 129597 73157.5 56439.5
    CDK2AP2 Rooted Divided doc-1 related protein (doc-1r). [swissprot;acc:o75956] 27.9136 37.2872 1.33581
    GNAI1 Ranked guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 267.144 336.073 1.25802
    KCNIP1 Subtracted kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 319.651 53.965
    MAGEA10 Squared Divided melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 219048 129762 1.68808
    PPP2R5A Measured Subtracted serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 17738.5 13995.7 3742.8
    PYGM Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 63.8686 47.2654 16.6032
    72 BRAF Measured b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 13977.7 3733.2
    C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 48429.6
    DTX2 Rooted deltex 2. [refseq;acc:nm_020892] 27.634 43.9629 16.3289
    GNAI3 Ranked Divided guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 267.144 336.073 1.25802
    KCNIP4 Subtracted potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 53.907
    MAGEB4 Squared Divided melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 219048 129762 1.68808
    NEUROD6 Rooted neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 27.9136 37.2872 1.33581
    PPP2R2D Measured uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 4556.79 2945.28 1.54715
    73 DTX1 Rooted Subtracted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 27.7078 44.017 16.3092
    JPH3 Ranked Divided junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 288 362 1.25694
    KCNIP2 Subtracted kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 265.632 319.531 53.899

    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/