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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1836 to 1885 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
network_comparison
green
1836 RPIA ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 208.821 1.01125 211.17
1837 KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 218.984 1.01124 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] 221.525 1.01118 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] 211.882 1.01116 209.544
1841 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 212.455 1.01115 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] 214.773 1.01109 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] 217.077 1.01106 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] 217.066 1.01103 214.698
1847 no value brain protein 16. [refseq;acc:nm_016458] 216.811 1.011 219.195
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] 218.445 1.01097 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] 218.448 1.01096 216.08
1852 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 196.008 1.01095 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] 222.215 1.0109 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] 217.893 1.01089 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] 210.856 1.01087 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] 203.071 1.01086 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] 207.642 1.01085 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] 220.107 1.01082 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] 222.819 1.01081 225.228
1872 POLDIP2 dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
1873 no value 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 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] 212.186 1.01075 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]
1880 CDA cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 220.852 1.01074 223.225
1881 no value 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 RPL28 60s ribosomal protein l28. [swissprot;acc:p46779] 215.896 1.0107 213.61
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] 240.317 1.01067 242.881
1884 OLA1 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 215.081 1.01066 217.373
1885 ARG1 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 204.44 1.01064 206.615

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/