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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1862 to 1911 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] CYB5R1 210.856 213.147 1.01087
    1863 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] CYB5R3
    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] PUF60 203.071 200.89 1.01086
    1865 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] EIF2S3 221.639 224.046
    1866 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] EIF2B4 221.725 224.133
    1867 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] no value 203.071 200.89
    1868 protein kinase nyd-sp25. [refseq;acc:nm_033516] TPD52L3 207.642 209.895 1.01085
    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] LANCL2 220.107 217.75 1.01082
    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] LANCL1
    1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] CLPX 222.819 225.228 1.01081
    1872 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] POLDIP2
    1873 scratch; scratch 1. [refseq;acc:nm_031309] no value 210.55 208.305 1.01078
    1874 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 223.862 226.271 1.01076
    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] NSUN5
    1876 williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] NSUN5B
    1877 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] NUCB1 212.186 214.467 1.01075
    1878 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] MLH1
    1879 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] NUCB2
    1880 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] CDA 220.852 223.225 1.01074
    1881 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] no value 210.592 208.355
    1882 60s ribosomal protein l28. [swissprot;acc:p46779] RPL28 215.896 213.61 1.0107
    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] PFKP 240.317 242.881 1.01067
    1884 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] OLA1 215.081 217.373 1.01066
    1885 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] ARG1 204.44 206.615 1.01064
    1886 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] ARG2 204.512 206.682 1.01061
    1887 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] SARM1 220.896 218.577
    1888 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] ICT1 218.414 216.131 1.01056
    1889 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] RAB3IL1 211.27 209.067 1.01054
    1890 rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] RAB3IP 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] MCM3 233.828 231.395 1.01051
    1892 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] KEAP1
    1893 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] GMPPB 222.842 225.17 1.01045
    1894 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] GMPPA
    1895 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] CAP2 215.853 213.639 1.01036
    1896 lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] LDB2 199.883 197.835 1.01035
    1897 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] no value
    1898 lim/homeobox protein lhx4. [swissprot;acc:q969g2] LHX4 199.881 197.833
    1899 lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] LHX3 199.884 197.837
    1900 solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] SLC27A4 191.401 193.38 1.01034
    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] TM7SF2 191.411 193.39
    1902 lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] LBR
    1903 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] SLC27A3 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] SLC27A2 191.424 193.404
    1905 disrupter of silencing 10. [refseq;acc:nm_020368] UTP3 191.411 193.39
    1906 very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] SLC27A6 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] SLC27A5 191.408 193.387
    1908 similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] DIP2B 191.415 193.394
    1909 calmegin precursor. [swissprot;acc:o14967] CLGN 217.48 215.256 1.01033
    1910 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] CANX
    1911 soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] SEPSECS

    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/