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 green red network_comparison
    Results: HTML CSV LaTeX Showing element 151 to 200 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Interaction Map
    		green
    		red
    		network_comparison
    19 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Ranked Low confidence 246.824 304.548 1.23387
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Squared 473408 332411 1.42416
    20 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 424645 299771 1.41656
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked High confidence 245.247 185.678 1.32082
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 24.2744 40.3337 1.66157
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 71.1231 57.2538 1.24224
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured High confidence 1865.5 677.5 2.75351
    Squared 823.69 108.641 7.58176
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Measured Low confidence 9368.87 7256.71 1.29106
    trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Ranked 246.737 304.359 1.23354
    21 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Measured 3917.88 3035.43 1.29072
    ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] High confidence 1865.5 677.5 2.75351
    Squared 823.69 108.641 7.58176
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 24.2744 40.3337 1.66157
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 185.678 1.32082
    n33 protein. [swissprot;acc:q13454] Rooted Low confidence 71.1231 57.2538 1.24224
    phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Ranked 163 198 1.21472
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared 134787 189688 1.40732
    22 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 57685.7 80340.8 1.39273
    cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Measured 3997.02 3126.88 1.27828
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked High confidence 245.247 185.678 1.32082
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 24.2915 40.3357 1.66049
    implantation-associated protein. [refseq;acc:nm_032121] Low confidence 71.1231 57.2538 1.24224
    n33 protein. [swissprot;acc:q13454] Ranked 163 198 1.21472
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Measured High confidence 1865.5 677.5 2.75351
    Squared 823.69 108.641 7.58176
    23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Ranked 44 58 1.31818
    carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Measured Low confidence 32028.5 40899 1.27696
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 76.7316 63.2736 1.2127
    gbp protein isoform a. [refseq;acc:nm_017870] Measured High confidence 1894.39 699.76 2.7072
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted 24.2919 40.3358 1.66046
    implantation-associated protein. [refseq;acc:nm_032121] Ranked Low confidence 163 198 1.21472
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 57169.1 78998 1.38183
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 457.521 143.692 3.18404
    24 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured Low confidence 4577.5 5720.25 1.24965
    bcl2-related ovarian killer. [refseq;acc:nm_032515] Rooted 61.2591 50.6099 1.21042
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Squared High confidence 457.521 143.692 3.18404
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted 24.2941 40.336 1.66032
    histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Ranked Low confidence 228.509 188.298 1.21355
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 57161.1 78977.2 1.38166
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked High confidence 44 58 1.31818
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 2108.52 950.561 2.21818
    25 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Ranked Low confidence 238.476 286.396 1.20094
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 56522.1 77316.3 1.3679
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 457.521 143.692 3.18404
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 24.295 40.3361 1.66026
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 892.67 1833.01 2.0534
    histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Low confidence 4691.96 5847.46 1.24627
    Rooted 56.875 67.7094 1.19049
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked High confidence 44 58 1.31818

    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/