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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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 description Value Type Network Comparison Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 1825 to 1874 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
green
network_comparison
red
1825 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 200.086 1.0115 202.386
1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 200.094 1.01149 202.393
1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 189.219 1.01147 191.39
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 200.115 202.41
1829 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 215.323 1.01146 212.884
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] 243.069 1.01144 240.32
1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 212.328 1.01139 214.746
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] 182.459 1.01136 180.409
1833 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
1834 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
1835 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 192.396 1.01132 194.573
1836 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 211.17 1.01125 208.821
1837 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 221.446 1.01124 218.984
1838 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
1839 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 224.001 1.01118 221.525
1840 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 209.544 1.01116 211.882
1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 210.113 1.01115 212.455
1842 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
1843 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
1844 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] 212.417 1.01109 214.773
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] 214.702 1.01106 217.077
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] 214.698 1.01103 217.066
1847 brain protein 16. [refseq;acc:nm_016458] 219.195 1.011 216.811
1848 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 216.064 218.441
1849 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 216.074 1.01097 218.445
1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 213.587 215.931
1851 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 216.08 1.01096 218.448
1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 198.154 1.01095 196.008
1853 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 215.564 217.924
1854 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 224.637 1.0109 222.215
1855 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 215.542 217.891
1856 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 215.543 217.892
1857 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 224.637 222.215
1858 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 215.545 1.01089 217.893
1859 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 215.547 217.895
1860 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
1861 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 213.147 1.01087 210.856
1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
1863 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
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] 200.89 1.01086 203.071
1865 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 224.046 221.639
1866 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] 224.133 221.725
1867 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 200.89 203.071
1868 protein kinase nyd-sp25. [refseq;acc:nm_033516] 209.895 1.01085 207.642
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] 217.75 1.01082 220.107
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]
1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 225.228 1.01081 222.819
1872 dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
1873 scratch; scratch 1. [refseq;acc:nm_031309] 208.305 1.01078 210.55
1874 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 226.271 1.01076 223.862

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
- 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/