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 red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
1841 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Subtracted 217.066 2.368 214.698
1842 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Divided 212.455 1.01115 210.113
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Subtracted 217.924 2.36 215.564
1843 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 2.357 217.75
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Divided 212.455 1.01115 210.113
1844 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] Subtracted 220.107 2.357 217.75
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Divided 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
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Subtracted 214.773 2.356 212.417
1846 ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 208.821 2.349 211.17
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Divided 217.066 1.01103 214.698
1847 brain protein 16. [refseq;acc:nm_016458] 216.811 1.011 219.195
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Subtracted 217.891 2.349 215.542
1848 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Divided 218.441 1.011 216.064
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Subtracted 217.892 2.349 215.543
1849 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 217.893 2.348 215.545
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Divided 218.445 1.01097 216.074
1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 215.931 213.587
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Subtracted 217.895 2.348 215.547
1851 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Divided 218.448 1.01096 216.08
1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 196.008 1.01095 198.154
adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Subtracted 215.931 2.344 213.587
1853 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 212.455 2.342 210.113
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Divided 217.924 1.01095 215.564
1854 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Subtracted 212.455 2.342 210.113
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Divided 222.215 1.0109 224.637
1855 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 217.891 215.542
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Subtracted 212.455 2.342 210.113
1856 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 2.338 209.544
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Divided 217.892 1.0109 215.543
1857 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Subtracted 222.842 2.328 225.17
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Divided 222.215 1.0109 224.637
1858 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Subtracted 222.842 2.328 225.17
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Divided 217.893 1.01089 215.545
1859 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 217.895 215.547
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Subtracted 220.896 2.319 218.577
1860 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 202.386 2.3 200.086
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Divided 217.895 1.01089 215.547
1861 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 210.856 1.01087 213.147
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Subtracted 202.386 2.3 200.086
1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Divided 210.856 1.01087 213.147
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 202.393 2.299 200.094
1863 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 202.41 2.295 200.115
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Divided 210.856 1.01087 213.147
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] 203.071 1.01086 200.89
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Subtracted 215.081 2.292 217.373
1865 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 210.856 2.291 213.147
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided 221.639 1.01086 224.046
1866 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Subtracted 210.856 2.291 213.147

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/