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 1830 to 1879 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1830 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] PFKM 240.32 243.069 1.01144
    1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] no value 214.746 212.328 1.01139
    1832 solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] SLC4A1AP 180.409 182.459 1.01136
    1833 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] CKS2
    1834 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] CTNNAL1
    1835 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] GORASP2 194.573 192.396 1.01132
    1836 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] RPIA 208.821 211.17 1.01125
    1837 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] KHK 218.984 221.446 1.01124
    1838 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] no value
    1839 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] EIF2S2 221.525 224.001 1.01118
    1840 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] APEX1 211.882 209.544 1.01116
    1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] PARL 212.455 210.113 1.01115
    1842 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] BBOX1
    1843 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] ATP11A
    1844 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] PAX6 214.773 212.417 1.01109
    1845 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] ABI2 217.077 214.702 1.01106
    1846 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] ABI1 217.066 214.698 1.01103
    1847 brain protein 16. [refseq;acc:nm_016458] no value 216.811 219.195 1.011
    1848 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] BAAT 218.441 216.064
    1849 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] ACOT1 218.445 216.074 1.01097
    1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] CAP1 215.931 213.587
    1851 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] ACOT4 218.448 216.08 1.01096
    1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] no value 196.008 198.154 1.01095
    1853 tubulin-tyrosine ligase. [refseq;acc:nm_153712] TTL 217.924 215.564
    1854 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] EIF2B5 222.215 224.637 1.0109
    1855 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] GRSF1 217.891 215.542
    1856 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] HNRPH3 217.892 215.543
    1857 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] EIF2B3 222.215 224.637
    1858 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] HNRPF 217.893 215.545 1.01089
    1859 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] HNRPH1 217.895 215.547
    1860 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] HNRPH2
    1861 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] CYB5R2 210.856 213.147 1.01087
    1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] CYB5R1
    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

    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/