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 [...,...].
    Gene Rank description Hugo Network Comparison Type Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 551 to 600 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		Interaction Map
    		green
    		network_comparison
    69 spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Measured 6475.5 High confidence 10307.5 1.59177
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Ranked 259.517 Low confidence 235.017 1.10425
    70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 Measured 6475.5 High confidence 10307.5 1.59177
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 Rooted 27.9136 37.2872 1.33581
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 Ranked 267.142 336.074 1.25804
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Squared 219048 129762 1.68808
    phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] PLAA 80538.1 Low confidence 64191.7 1.25465
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Rooted 61.9982 68.2337 1.10058
    y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] SLC7A7 Measured 6991.78 7848.45 1.12253
    71 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Squared 63411.7 51068.8 1.24169
    cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Ranked 230.944 209.149 1.10421
    cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] SLC7A11 Measured 6991.78 7848.45 1.12253
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Rooted 27.9136 High confidence 37.2872 1.33581
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 Ranked 267.144 336.073 1.25802
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Squared 219048 129762 1.68808
    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] no value Measured 4556.78 2945.26 1.54716
    tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] TAF2 Rooted 59.6397 Low confidence 65.6325 1.10048
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 Ranked 267.144 High confidence 336.073 1.25802
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Squared 219048 129762 1.68808
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Rooted 63.1259 Low confidence 69.4305 1.09987
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 27.9136 High confidence 37.2872 1.33581
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Squared 63404.8 Low confidence 51065.9 1.24163
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Ranked 230.944 209.149 1.10421
    solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] SLC7A6 Measured 6991.78 7848.45 1.12253
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D 4556.79 High confidence 2945.28 1.54715
    73 carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] CPN2 Squared 63279.6 Low confidence 51013.1 1.24046
    eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] EIF4B Measured 6991.78 7848.45 1.12253
    junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Ranked 288 High confidence 362 1.25694
    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] MAGED2 Squared 219048 129762 1.68808
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Rooted 27.9136 37.2872 1.33581
    rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 64.6594 Low confidence 71.0277 1.09849
    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] PPP2R2B Measured 4556.83 High confidence 2945.38 1.54711
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] SMYD1 Ranked 230.944 Low confidence 209.149 1.10421
    74 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] SLC7A9 Measured 6991.78 7848.45 1.12253
    diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] DGKH Rooted 62.2472 68.3765 1.09847
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Ranked 288 High confidence 362 1.25694
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Rooted 27.9136 37.2872 1.33581
    platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] GP5 Squared 63279.9 Low confidence 51013.3 1.24046
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Ranked 195.817 215.516 1.1006
    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] PPP2R2C Measured 4556.99 High confidence 2945.8 1.54694
    trophinin. [swissprot;acc:q12816] TRO Squared 219048 129762 1.68808
    75 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] BRAF 63087.3 Low confidence 50932.2 1.23865
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Rooted 27.9136 High confidence 37.2872 1.33581
    diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] DGKD 62.2472 Low confidence 68.3765 1.09847
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Squared 110342 High confidence 184298 1.67024
    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 Measured 1920.75 2907.43 1.5137
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS Ranked 249.709 Low confidence 226.944 1.10031
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Measured 11616 12942.3 1.11418
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 Ranked 288 High confidence 362 1.25694

    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/