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 green network_comparison
Results: HTML CSV LaTeX Showing element 1813 to 1862 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
1813 similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] 216.854 214.35 1.01168
1814 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 122.3 123.727 1.01167
1815 dpy-30-like protein. [swissprot;acc:q9c005] 220.462 217.926 1.01164
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] 218.36 215.874 1.01152
1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 240.32 243.085 1.01151
1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 202.386 200.086 1.0115
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] 202.393 200.094 1.01149
1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 191.39 189.219 1.01147
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] 212.884 215.323 1.01146
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] 240.32 243.069 1.01144
1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 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] 180.409 182.459 1.01136
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] 194.573 192.396 1.01132
1836 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 208.821 211.17 1.01125
1837 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 218.984 221.446 1.01124
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] 221.525 224.001 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] 211.882 209.544 1.01116
1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 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]
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] 214.773 212.417 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] 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] 217.066 214.698 1.01103
1847 brain protein 16. [refseq;acc:nm_016458] 216.811 219.195 1.011
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] 218.445 216.074 1.01097
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] 218.448 216.08 1.01096
1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 196.008 198.154 1.01095
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] 222.215 224.637 1.0109
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] 217.893 215.545 1.01089
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] 210.856 213.147 1.01087
1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]

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/