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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 558 to 607 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    70 Squared phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence PLAA 1.25465 80538.1 64191.7
    Rooted chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] High confidence CHD3 1.33581 27.9136 37.2872
    transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence TFDP2 1.10058 61.9982 68.2337
    71 Measured cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] SLC7A11 1.12253 6991.78 7848.45
    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] High confidence no value 1.54716 4556.78 2945.26
    Ranked cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Low confidence 1.10421 230.944 209.149
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] High confidence GNAI1 1.25802 267.144 336.073
    Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Low confidence ARAF 1.24169 63411.7 51068.8
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] High confidence MAGEA10 1.68808 219048 129762
    Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 1.33581 27.9136 37.2872
    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] Low confidence TAF2 1.10048 59.6397 65.6325
    72 Measured solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] SLC7A6 1.12253 6991.78 7848.45
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence PPP2R2D 1.54715 4556.79 2945.28
    Ranked guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 1.25802 267.144 336.073
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Low confidence SMYD2 1.10421 230.944 209.149
    Squared melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] High confidence MAGEB4 1.68808 219048 129762
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Low confidence RAF1 1.24163 63404.8 51065.9
    Rooted mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 1.09987 63.1259 69.4305
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence NEUROD6 1.33581 27.9136 37.2872
    73 Measured eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence EIF4B 1.12253 6991.78 7848.45
    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] High confidence PPP2R2B 1.54711 4556.83 2945.38
    Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 1.25694 288 362
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence SMYD1 1.10421 230.944 209.149
    Squared carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] CPN2 1.24046 63279.6 51013.1
    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] High confidence MAGED2 1.68808 219048 129762
    Rooted neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 1.33581 27.9136 37.2872
    rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence RINT1 1.09849 64.6594 71.0277
    74 Measured b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] SLC7A9 1.12253 6991.78 7848.45
    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] High confidence PPP2R2C 1.54694 4556.99 2945.8
    Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 1.25694 288 362
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Low confidence AHCYL1 1.1006 195.817 215.516
    Squared platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] GP5 1.24046 63279.9 51013.3
    trophinin. [swissprot;acc:q12816] High confidence TRO 1.68808 219048 129762
    Rooted diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence DGKH 1.09847 62.2472 68.3765
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence NEUROD4 1.33581 27.9136 37.2872
    75 Measured 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 1.5137 1920.75 2907.43
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence SEPT7 1.11418 11616 12942.3
    Ranked nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS 1.10031 249.709 226.944
    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] High confidence SMPD2 1.25694 288 362
    Squared b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Low confidence BRAF 1.23865 63087.3 50932.2
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence MYO5B 1.67024 110342 184298
    Rooted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 1.33581 27.9136 37.2872
    diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence DGKD 1.09847 62.2472 68.3765
    76 Measured protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] PPP1R14A 1.11235 5334.13 5933.4
    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] High confidence PPP2R1B 1.50373 4599.26 3058.57
    Ranked db83 protein. [swissprot;acc:p57088] TMEM33 1.25694 288 362
    nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence NIPSNAP1 1.10017 249.584 226.86
    Squared myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence MYO5C 1.67024 110342 184298
    pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Low confidence PANK3 1.23831 52172 64605
    Rooted cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] High confidence CDK2AP1 1.33581 27.9136 37.2872

    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/