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 Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1232 to 1281 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    616 Subtracted CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 12.542
    617 Divided HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 214.257 202.135 1.05997
    Subtracted CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] 177.698 190.239 12.541
    618 Divided GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
    Subtracted CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 177.699 190.24 12.541
    619 Divided FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 214.256 202.139 1.05994
    Subtracted VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 206.274 218.792 12.518
    620 Divided GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 214.256 202.14 1.05994
    Subtracted MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] 206.274 218.792 12.518
    621 Divided GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 214.256 202.14 1.05994
    Subtracted RPLP2 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 231.92 244.435 12.515
    622 Divided GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 214.256 202.14 1.05994
    Subtracted SYN3 synapsin iii. [swissprot;acc:o14994] 229.072 216.576 12.496
    623 Divided GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 214.256 202.14 1.05994
    Subtracted no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 229.072 216.576 12.496
    624 Divided interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 214.256 202.139 1.05994
    Subtracted HEY1 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] 229.072 216.576 12.496
    625 Divided GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 214.256 202.14 1.05994
    Subtracted ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 12.496
    626 Divided GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 214.256 202.14 1.05994
    Subtracted HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 12.496
    627 Divided JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 214.256 202.139 1.05994
    Subtracted SYN2 synapsin ii. [swissprot;acc:q92777] 229.072 216.576 12.496
    628 Divided GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 214.256 202.14 1.05994
    Subtracted MRRF mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 229.072 216.576 12.496
    629 Divided GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
    Subtracted PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 12.496
    630 Divided NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 214.256 202.141 1.05993
    Subtracted HEY2 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 12.496
    631 Divided PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
    Subtracted HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 229.072 216.576 12.496
    632 Divided HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 214.254 202.166 1.05979
    Subtracted ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 229.072 216.576 12.496
    633 Divided AARS alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 234.106 248.104 1.05979
    Subtracted ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 229.072 216.576 12.496
    634 Divided no value dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
    Subtracted SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] 229.072 216.576 12.496
    635 Divided RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 228.639 242.258 1.05957
    Subtracted MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 235.296 247.673 12.377
    636 Divided SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] 228.639 242.258 1.05957
    Subtracted VAV1 vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 12.351
    637 Divided PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 228.639 242.258 1.05957
    Subtracted VAV3 vav-3 protein. [swissprot;acc:q9ukw4] 212.253 199.908 12.345
    638 Divided SNX17 sorting nexin 17. [swissprot;acc:q15036] 228.639 242.258 1.05957
    Subtracted VAV2 vav-2 protein. [swissprot;acc:p52735] 212.526 200.212 12.314
    639 Divided HRB nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 217.67 230.596 1.05938
    Subtracted NOVA1 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] 222.554 234.847 12.293
    640 Divided no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 217.67 230.596 1.05938
    Subtracted histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 12.265
    641 Divided PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 217.67 230.596 1.05938

    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/