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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 486 to 535 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    31 Divided MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted Low confidence 145.551 1.1597 168.796
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] High confidence 26.0288 1.65937 43.1914
    PPP2R2B 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] Ranked 187.458 1.2999 243.677
    Subtracted no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 142 28 170
    GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] High confidence 267.14 68.935 336.075
    HINT1 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] Rooted Low confidence 67.7094 10.8344 56.875
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured High confidence 23693.7 5430.7 18263
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Squared 106226 85915 192141
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Low confidence 92920.4 21124 71796.4
    TUSC3 n33 protein. [swissprot;acc:q13454] Measured 3278 1780.5 5058.5
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted High confidence 40.0958 18.7028 58.7986
    32 Divided no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured 1834.73 2.04793 895.893
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 36360.3 1.19275 43368.8
    ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared High confidence 9924.76 2.53372 25146.6
    FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted 26.0288 1.65937 43.1914
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared Low confidence 82347.8 1.33073 61881.5
    PPP2R2C 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] Ranked High confidence 187.462 1.29985 243.673
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Low confidence 273.188 1.17505 232.49
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 1.1597 168.796
    Subtracted no value implantation-associated protein. [refseq;acc:nm_032121] Measured 3278 1780.5 5058.5
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] High confidence 23693.7 5430.7 18263
    GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 267.142 68.932 336.074
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 106226 85915 192141
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Low confidence 92262.9 20862.7 71400.2
    RGS12 regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Ranked 247.768 27.927 219.841
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Rooted High confidence 23.9771 18.5002 42.4773
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Low confidence 38.4152 10.7377 49.1529
    33 Divided no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 82347.8 1.33073 61881.5
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Rooted High confidence 26.0288 1.65937 43.1914
    BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Measured Low confidence 36360.3 1.19275 43368.8
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 1835.3 2.04611 896.972
    MAP2K4 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Ranked Low confidence 210.241 1.17068 246.125
    PPP2R1B 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 188.688 1.28647 242.742
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 9924.76 2.53372 25146.6
    UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Rooted Low confidence 76.5734 1.15738 88.6244
    Subtracted ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 77316.3 20794.2 56522.1
    GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked High confidence 267.144 68.929 336.073
    GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 228.147 27.597 200.55
    MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured High confidence 23693.7 5430.7 18263
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared 106226 85915 192141
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 25.6987 17.8623 43.561
    SEPT6 septin 6. [swissprot;acc:q14141] Measured Low confidence 13005.8 1767.9 14773.7
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted 38.5678 10.6955 49.2633
    34 Divided AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Squared High confidence 9924.76 2.53372 25146.6
    GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured 1836.71 2.02382 907.546
    Rooted 40.2812 1.65305 24.3678
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared Low confidence 82347.8 1.33073 61881.5
    PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Ranked High confidence 189.07 1.28235 242.453
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Rooted Low confidence 49.0544 1.15698 56.755
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Ranked 155.56 1.16197 133.876

    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/