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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1230 to 1279 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    615 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] HOXB9 Divided 214.257 202.132 1.05999
    616 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] HOXA9
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 Subtracted 177.698 190.24 12.542
    617 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 190.239 12.541
    homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] HOXC9 Divided 214.257 202.135 1.05997
    618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] GABRG3 214.256 202.139 1.05994
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Subtracted 177.699 190.24 12.541
    619 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] FOXG1 Divided 214.256 202.139 1.05994
    vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] VPS39 Subtracted 206.274 218.792 12.518
    620 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] GABRG1 Divided 214.256 202.14 1.05994
    microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] MAP4 Subtracted 206.274 218.792 12.518
    621 60s acidic ribosomal protein p2. [swissprot;acc:p05387] RPLP2 231.92 244.435 12.515
    gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] GABRA2 Divided 214.256 202.14 1.05994
    622 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] GABRA6
    synapsin iii. [swissprot;acc:o14994] SYN3 Subtracted 229.072 216.576 12.496
    623 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] no value
    gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] GABRG2 Divided 214.256 202.14 1.05994
    624 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] HEY1 Subtracted 229.072 216.576 12.496
    interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] no value Divided 214.256 202.139 1.05994
    625 actin binding lim protein 2. [refseq;acc:nm_032432] ABLIM2 Subtracted 229.072 216.576 12.496
    gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] GABRA4 Divided 214.256 202.14 1.05994
    626 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] GABRE
    hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] HEYL Subtracted 229.072 216.576 12.496
    627 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] JMJD6 Divided 214.256 202.139 1.05994
    synapsin ii. [swissprot;acc:q92777] SYN2 Subtracted 229.072 216.576 12.496
    628 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] GABRA1 Divided 214.256 202.14 1.05994
    mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] MRRF Subtracted 229.072 216.576 12.496
    629 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] GABRA3 Divided 214.256 202.14 1.05994
    peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] PEX5 Subtracted 229.072 216.576 12.496
    630 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] HEY2
    nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] NDUFA6 Divided 214.256 202.141 1.05993
    631 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] PDXDC1
    transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] HES1 Subtracted 229.072 216.576 12.496
    632 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] ECH1
    homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] HOXD9 Divided 214.254 202.166 1.05979
    633 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] ABLIM1 Subtracted 229.072 216.576 12.496
    alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] AARS Divided 234.106 248.104 1.05979
    634 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] no value 226.523 213.786 1.05958
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] SYN1 Subtracted 229.072 216.576 12.496
    635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] RPL37 Divided 228.639 242.258 1.05957
    mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] MVK Subtracted 235.296 247.673 12.377
    636 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] SFRS1 Divided 228.639 242.258 1.05957
    vav proto-oncogene. [swissprot;acc:p15498] VAV1 Subtracted 212.2 199.849 12.351
    637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] PPAT Divided 228.639 242.258 1.05957
    vav-3 protein. [swissprot;acc:q9ukw4] VAV3 Subtracted 212.253 199.908 12.345
    638 sorting nexin 17. [swissprot;acc:q15036] SNX17 Divided 228.639 242.258 1.05957
    vav-2 protein. [swissprot;acc:p52735] VAV2 Subtracted 212.526 200.212 12.314
    639 nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] HRB Divided 217.67 230.596 1.05938
    rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] NOVA1 Subtracted 222.554 234.847 12.293
    640 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] no value 244.842 232.577 12.265

    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/