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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Value Type Interaction Map Filtered Gene Rank green description red network_comparison Network Comparison Type
Results: HTML CSV LaTeX Showing element 1808 to 1857 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
Rank
green
description
red
network_comparison
1808 208.651 ral-a exchange factor ralgps2. [refseq;acc:nm_152663] 211.102 1.01175
1809 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]
1810 225.827 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 223.214 1.01171
1811 214.35 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] 216.854 1.01168
1812 214.564 cyclin c. [swissprot;acc:p24863] 217.071
1813 214.35 similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] 216.854
1814 123.727 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 122.3 1.01167
1815 217.926 dpy-30-like protein. [swissprot;acc:q9c005] 220.462 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 215.874 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] 218.36 1.01152
1822 243.085 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
1823 200.086 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 202.386 1.0115
1824 212.281 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 214.722
1825 200.086 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 202.386
1826 200.094 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 202.393 1.01149
1827 189.219 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
1828 200.115 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 202.41
1829 215.323 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
1830 243.069 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
1831 212.328 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 214.746 1.01139
1832 182.459 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
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 192.396 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 194.573 1.01132
1836 211.17 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 208.821 1.01125
1837 221.446 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 218.984 1.01124
1838 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
1839 224.001 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 221.525 1.01118
1840 209.544 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
1841 210.113 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 212.455 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 212.417 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] 214.773 1.01109
1845 214.702 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
1846 214.698 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
1847 219.195 brain protein 16. [refseq;acc:nm_016458] 216.811 1.011
1848 216.064 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 218.441
1849 216.074 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
1850 213.587 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 215.931
1851 216.08 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 218.448 1.01096
1852 198.154 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 196.008 1.01095
1853 215.564 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 217.924
1854 224.637 translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 222.215 1.0109
1855 215.542 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 217.891
1856 215.543 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 217.892
1857 224.637 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 222.215

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/