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 [...,...].
    Gene Rank Hugo description Network Comparison Type Value Type Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1830 to 1879 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		network_comparison
    		red
    		green
    1830 PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 1.01144 240.32 243.069
    1831 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 1.01139 214.746 212.328
    1832 SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 1.01136 180.409 182.459
    1833 CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
    1834 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
    1835 GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 1.01132 194.573 192.396
    1836 RPIA ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 1.01125 208.821 211.17
    1837 KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 1.01124 218.984 221.446
    1838 no value purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
    1839 EIF2S2 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 1.01118 221.525 224.001
    1840 APEX1 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 1.01116 211.882 209.544
    1841 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 1.01115 212.455 210.113
    1842 BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
    1843 ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
    1844 PAX6 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] 1.01109 214.773 212.417
    1845 ABI2 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] 1.01106 217.077 214.702
    1846 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 1.01103 217.066 214.698
    1847 no value brain protein 16. [refseq;acc:nm_016458] 1.011 216.811 219.195
    1848 BAAT bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 218.441 216.064
    1849 ACOT1 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 1.01097 218.445 216.074
    1850 CAP1 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 215.931 213.587
    1851 ACOT4 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 1.01096 218.448 216.08
    1852 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1.01095 196.008 198.154
    1853 TTL tubulin-tyrosine ligase. [refseq;acc:nm_153712] 217.924 215.564
    1854 EIF2B5 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 1.0109 222.215 224.637
    1855 GRSF1 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 217.891 215.542
    1856 HNRPH3 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 217.892 215.543
    1857 EIF2B3 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 222.215 224.637
    1858 HNRPF heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 1.01089 217.893 215.545
    1859 HNRPH1 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 217.895 215.547
    1860 HNRPH2 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
    1861 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1.01087 210.856 213.147
    1862 CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
    1863 CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
    1864 PUF60 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] 1.01086 203.071 200.89
    1865 EIF2S3 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 EIF2B4 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] 221.725 224.133
    1867 no value multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 203.071 200.89
    1868 TPD52L3 protein kinase nyd-sp25. [refseq;acc:nm_033516] 1.01085 207.642 209.895
    1869 LANCL2 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] 1.01082 220.107 217.75
    1870 LANCL1 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 CLPX atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 1.01081 222.819 225.228
    1872 POLDIP2 dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
    1873 no value scratch; scratch 1. [refseq;acc:nm_031309] 1.01078 210.55 208.305
    1874 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 1.01076 223.862 226.271
    1875 NSUN5 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 NSUN5B williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
    1877 NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1.01075 212.186 214.467
    1878 MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
    1879 NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]

    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/