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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1858 to 1907 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		network_comparison
    		green
    1858 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 217.893 1.01089 215.545
    1859 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 217.895 215.547
    1860 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
    1861 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 210.856 1.01087 213.147
    1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
    1863 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
    1864 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 203.071 1.01086 200.89
    1865 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 221.639 224.046
    1866 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] 221.725 224.133
    1867 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 203.071 200.89
    1868 protein kinase nyd-sp25. [refseq;acc:nm_033516] 207.642 1.01085 209.895
    1869 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 220.107 1.01082 217.75
    1870 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]
    1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 222.819 1.01081 225.228
    1872 dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
    1873 scratch; scratch 1. [refseq;acc:nm_031309] 210.55 1.01078 208.305
    1874 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 223.862 1.01076 226.271
    1875 williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
    1876 williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
    1877 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 212.186 1.01075 214.467
    1878 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
    1879 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]
    1880 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 220.852 1.01074 223.225
    1881 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 210.592 208.355
    1882 60s ribosomal protein l28. [swissprot;acc:p46779] 215.896 1.0107 213.61
    1883 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 240.317 1.01067 242.881
    1884 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 215.081 1.01066 217.373
    1885 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 204.44 1.01064 206.615
    1886 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 204.512 1.01061 206.682
    1887 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] 220.896 218.577
    1888 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 218.414 1.01056 216.131
    1889 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 211.27 1.01054 209.067
    1890 rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 211.314 209.111
    1891 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 233.828 1.01051 231.395
    1892 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145]
    1893 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 222.842 1.01045 225.17
    1894 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
    1895 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 215.853 1.01036 213.639
    1896 lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] 199.883 1.01035 197.835
    1897 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
    1898 lim/homeobox protein lhx4. [swissprot;acc:q969g2] 199.881 197.833
    1899 lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] 199.884 197.837
    1900 solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] 191.401 1.01034 193.38
    1901 delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] 191.411 193.39
    1902 lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
    1903 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] 191.406 193.385
    1904 very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] 191.424 193.404
    1905 disrupter of silencing 10. [refseq;acc:nm_020368] 191.411 193.39
    1906 very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] 191.41 193.389
    1907 solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] 191.408 193.387

    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
    - 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/