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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 3730 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		description
    		Filtered
    		red
    		green
    		network_comparison
    51 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 779.167 1390.33 1.78438
    ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 184.422 88.5622 2.0824
    52 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 1 779.167 1390.33 1.78438
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 0 999.28 481.725 2.07438
    53 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] 1 779.167 1390.33 1.78438
    muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 420.365 861.814 2.05016
    54 deltex 2. [refseq;acc:nm_020892] 1 1618.84 2651.88 1.63814
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 0 638.862 330.189 1.93484
    55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1 1629.21 2662.12 1.63399
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 0 630.942 327.517 1.92644
    56 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] 1 1631.67 2664.55 1.63302
    tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 0 271.484 142.981 1.89874
    57 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 270.264 142.417 1.89769
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 1631.67 2664.55 1.63302
    58 40s ribosomal protein s26. [swissprot;acc:p02383] 0 150.741 81.2233 1.85588
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 1631.67 2664.55 1.63302
    59 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 0 150.673 279.24 1.85328
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1 1631.67 2664.55 1.63302
    60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
    adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 0 47.4756 87.5499 1.8441
    61 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 324.442 593.094 1.82804
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 4489.19 2765.82 1.6231
    62 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 210.767 384.407 1.82385
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 4489.19 2765.82 1.6231
    63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
    spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 31.1429 56.278 1.80709
    64 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 4489.19 2765.82 1.6231
    phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 0.00001 18 1800000
    65 neuralized-like. [refseq;acc:nm_004210] 1 1657.68 2690.25 1.6229
    rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 18 0.00001 1800000
    66 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] 1 1991.03 3221.38 1.61795
    soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 688.436 385.626 1.78524
    67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 6475.5 10307.5 1.59177
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 1603 898 1.78508
    68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 1 6475.5 10307.5 1.59177
    protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 0 198.964 351.772 1.76802
    69 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1593 2804 1.7602
    spermatogenesis associated 6. [refseq;acc:nm_019073] 1 6475.5 10307.5 1.59177
    70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
    importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 0 607 1068 1.75947
    71 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] 1 4556.78 2945.26 1.54716
    ubiquitin protein ligase. [refseq;acc:nm_130466] 0 620 352.75 1.75762
    72 60s ribosomal protein l21. [swissprot;acc:p46778] 572 992.083 1.73441
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 4556.79 2945.28 1.54715
    73 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 65.2968 37.693 1.73233
    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] 1 4556.83 2945.38 1.54711
    74 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 0 501.151 859.34 1.71473
    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] 1 4556.99 2945.8 1.54694
    75 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] 1920.75 2907.43 1.5137
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 1586.07 925.298 1.71412

    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
    - 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/