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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 501 to 550 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    32 ARRB1 Divided 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
    GNAI2 Subtracted 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
    MAGEA2B Divided melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared Low confidence 82347.8 1.33073 61881.5
    PANK1 Subtracted pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 106226 85915 192141
    PPP2R2C Divided 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 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
    PSCD4 Subtracted cytohesin 4. [swissprot;acc:q9uia0] Squared 92262.9 20862.7 71400.2
    RGS12 regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Ranked 247.768 27.927 219.841
    SLC25A43 Divided mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 1.1597 168.796
    TMEM132A Subtracted gbp protein isoform a. [refseq;acc:nm_017870] 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 no value Divided 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
    ATG4B Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Low confidence 77316.3 20794.2 56522.1
    BEST2 Divided vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Measured 36360.3 1.19275 43368.8
    GNAI1 Subtracted 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
    GNG11 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured 1835.3 2.04611 896.972
    GSTO2 Subtracted ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 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
    MAP2K4 Divided 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
    PANK2 Subtracted pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared High confidence 106226 85915 192141
    PPP2R1B Divided 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] Ranked 188.688 1.28647 242.742
    PRKRAP1 Subtracted 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
    SPATA6 Divided spermatogenesis associated 6. [refseq;acc:nm_019073] Squared High confidence 9924.76 2.53372 25146.6
    TOB1 Subtracted tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted Low confidence 38.5678 10.6955 49.2633
    UBR4 Divided retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 76.5734 1.15738 88.6244
    34 no value Subtracted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 140.508 17.63 122.878
    AMPD2 Divided amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Squared 9924.76 2.53372 25146.6
    ATF3 Subtracted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured Low confidence 5492.04 1758.96 7251
    BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Rooted 50.6099 10.6492 61.2591
    GNA11 Divided guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured High confidence 1836.71 2.02382 907.546
    Rooted 40.2812 1.65305 24.3678
    GNAI3 Subtracted guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked 267.144 68.929 336.073
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Low confidence 227.371 26.839 200.532
    MAGEA6 Divided melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 82347.8 1.33073 61881.5
    MAGEA8 Subtracted melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured High confidence 23693.7 5430.7 18263
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared Low confidence 82347.8 20466.3 61881.5
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 106226 85915 192141
    PPP2R1A Divided 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 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
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Measured 5339.5 1.1897 6352.4
    35 ATG3 Subtracted apg3p; pc3-96 protein. [refseq;acc:nm_022488] Rooted High confidence 140.508 17.63 122.878
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Low confidence 267.448 26.626 240.822
    DNASE2B Divided deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 33111.4 1.18866 39358.1
    GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 1836.71 2.02378 907.564
    Rooted 40.2812 1.65304 24.3679
    GNB5 Subtracted guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Ranked 267.636 67.723 335.359

    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/