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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    32 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Subtracted GNAI2 Ranked High confidence 267.142 336.074 68.932
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided no value Measured 1834.73 895.893 2.04793
    implantation-associated protein. [refseq;acc:nm_032121] Subtracted Low confidence 3278 5058.5 1780.5
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided MAGEA2B Squared 82347.8 61881.5 1.33073
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted no value Measured High confidence 23693.7 18263 5430.7
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided SLC25A43 Rooted Low confidence 145.551 168.796 1.1597
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Measured 36360.3 43368.8 1.19275
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Subtracted PANK1 Squared High confidence 106226 192141 85915
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided PRKRAP1 Ranked Low confidence 273.188 232.49 1.17505
    regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Subtracted RGS12 247.768 219.841 27.927
    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] Divided PPP2R2C High confidence 187.462 243.673 1.29985
    tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Subtracted TOB2 Rooted Low confidence 38.4152 49.1529 10.7377
    33 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Ranked 228.147 200.55 27.597
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Squared 77316.3 56522.1 20794.2
    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] Divided MAP2K4 Ranked 210.241 246.125 1.17068
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Subtracted GNAI1 High confidence 267.144 336.073 68.929
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided GNG11 Measured 1835.3 896.972 2.04611
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value Squared Low confidence 82347.8 61881.5 1.33073
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted MAGEA9 Measured High confidence 23693.7 18263 5430.7
    pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Squared 106226 192141 85915
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 Rooted 25.6987 43.561 17.8623
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Divided no value 26.0288 43.1914 1.65937
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Low confidence 76.5734 88.6244 1.15738
    septin 6. [swissprot;acc:q14141] Subtracted SEPT6 Measured 13005.8 14773.7 1767.9
    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] Divided PPP2R1B Ranked High confidence 188.688 242.742 1.28647
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Squared 9924.76 25146.6 2.53372
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted TOB1 Rooted Low confidence 38.5678 49.2633 10.6955
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Divided BEST2 Measured 36360.3 43368.8 1.19275
    34 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 Squared High confidence 9924.76 25146.6 2.53372
    bcl2-related ovarian killer. [refseq;acc:nm_032515] Subtracted BOK Rooted Low confidence 50.6099 61.2591 10.6492
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 Measured 5492.04 7251 1758.96
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value Rooted High confidence 140.508 122.878 17.63
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Ranked Low confidence 227.371 200.532 26.839
    guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 High confidence 267.144 336.073 68.929
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided GNA11 Measured 1836.71 907.546 2.02382
    Rooted 40.2812 24.3678 1.65305
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Subtracted MAGED4 Squared Low confidence 82347.8 61881.5 20466.3
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided MAGEA6 1.33073
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted MAGEA8 Measured High confidence 23693.7 18263 5430.7
    pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] PANK3 Squared 106226 192141 85915
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided UFC1 Measured Low confidence 5339.5 6352.4 1.1897
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 Ranked 155.56 133.876 1.16197
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] RBM7 Rooted 49.0544 56.755 1.15698
    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] PPP2R1A Ranked High confidence 189.07 242.453 1.28235
    35 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Squared 106226 192141 1.80879
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted ATG3 Rooted 140.508 122.878 17.63
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Ranked Low confidence 267.448 240.822 26.626
    deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided DNASE2B Measured 33111.4 39358.1 1.18866
    guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Subtracted GNB5 Ranked High confidence 267.636 335.359 67.723
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided GNAQ Measured 1836.71 907.564 2.02378

    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/