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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1812 to 1861 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
network_comparison
green
1812 cyclin c. [swissprot;acc:p24863] 217.071 1.01168 214.564
1813 similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] 216.854 214.35
1814 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 122.3 1.01167 123.727
1815 dpy-30-like protein. [swissprot;acc:q9c005] 220.462 1.01164 217.926
1816 rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151]
1817 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
1818 neighbor of cox4. [swissprot;acc:o43402]
1819 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
1820 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
1821 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] 218.36 1.01152 215.874
1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 240.32 1.01151 243.085
1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 202.386 1.0115 200.086
1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 214.722 212.281
1825 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 202.386 200.086
1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 202.393 1.01149 200.094
1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 191.39 1.01147 189.219
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 202.41 200.115
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] 212.884 1.01146 215.323
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] 240.32 1.01144 243.069
1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 214.746 1.01139 212.328
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] 180.409 1.01136 182.459
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] 194.573 1.01132 192.396
1836 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 208.821 1.01125 211.17
1837 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 218.984 1.01124 221.446
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] 221.525 1.01118 224.001
1840 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 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 212.455 1.01115 210.113
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] 214.773 1.01109 212.417
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] 217.077 1.01106 214.702
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] 217.066 1.01103 214.698
1847 brain protein 16. [refseq;acc:nm_016458] 216.811 1.011 219.195
1848 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 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] 218.445 1.01097 216.074
1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 215.931 213.587
1851 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 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 196.008 1.01095 198.154
1853 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 217.924 215.564
1854 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 222.215 1.0109 224.637
1855 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 217.891 215.542
1856 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 217.892 215.543
1857 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 222.215 224.637
1858 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 217.893 1.01089 215.545
1859 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 217.895 215.547
1860 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
1861 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 210.856 1.01087 213.147

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/