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 Hugo description Value Type Network Comparison Type Interaction Map green Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 1880 to 1929 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		green
    		red
    		network_comparison
    1880 CDA cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 223.225 220.852 1.01074
    1881 no value dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 208.355 210.592
    1882 RPL28 60s ribosomal protein l28. [swissprot;acc:p46779] 213.61 215.896 1.0107
    1883 PFKP 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] 242.881 240.317 1.01067
    1884 OLA1 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 217.373 215.081 1.01066
    1885 ARG1 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 206.615 204.44 1.01064
    1886 ARG2 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 206.682 204.512 1.01061
    1887 SARM1 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] 218.577 220.896
    1888 ICT1 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 216.131 218.414 1.01056
    1889 RAB3IL1 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 209.067 211.27 1.01054
    1890 RAB3IP rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 209.111 211.314
    1891 MCM3 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 231.395 233.828 1.01051
    1892 KEAP1 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145]
    1893 GMPPB gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 225.17 222.842 1.01045
    1894 GMPPA gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
    1895 CAP2 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 213.639 215.853 1.01036
    1896 LDB2 lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] 197.835 199.883 1.01035
    1897 no value lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
    1898 LHX4 lim/homeobox protein lhx4. [swissprot;acc:q969g2] 197.833 199.881
    1899 LHX3 lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] 197.837 199.884
    1900 SLC27A4 solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] 193.38 191.401 1.01034
    1901 TM7SF2 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] 193.39 191.411
    1902 LBR lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
    1903 SLC27A3 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] 193.385 191.406
    1904 SLC27A2 very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] 193.404 191.424
    1905 UTP3 disrupter of silencing 10. [refseq;acc:nm_020368] 193.39 191.411
    1906 SLC27A6 very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] 193.389 191.41
    1907 SLC27A5 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] 193.387 191.408
    1908 DIP2B similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] 193.394 191.415
    1909 CLGN calmegin precursor. [swissprot;acc:o14967] 215.256 217.48 1.01033
    1910 CANX calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824]
    1911 SEPSECS soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]
    1912 RNMT rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]
    1913 no value phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 213.564 215.745 1.01021
    1914 PLSCR4 phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]
    1915 PLSCR2 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 213.571 215.747 1.01019
    1916 RHCG rh type c glycoprotein. [refseq;acc:nm_016321] 198.88 196.88 1.01016
    1917 ING5 p28 ing5. [refseq;acc:nm_032329] 218.039 215.848 1.01015
    1918 MED28 endothelial-derived gene 1. [refseq;acc:nm_025205] 200.18 202.211
    1919 HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 185.349 187.231
    1920 HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 185.413 187.292 1.01013
    1921 MTR 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 219.386 221.607 1.01012
    1922 CENTG2 centaurin gamma 2. [swissprot;acc:q9upq3] 218.452 220.659 1.0101
    1923 USO1 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763]
    1924 CENTG1 centaurin gamma 1. [swissprot;acc:q99490]
    1925 CENTG3 centaurin gamma 3. [swissprot;acc:q96p47]
    1926 RHBG rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] 198.91 196.925 1.01008
    1927 RHAG rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 198.914 196.932 1.01006
    1928 RHD blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 198.935 196.964 1.01001
    1929 no value enigma protein; lim domain protein. [refseq;acc:nm_005451] 217.574 219.753

    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/