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 green Interaction Map Gene Rank description Network Comparison Type Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 2325 to 2374 of 3228 in total
Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
green
Rank
description
red
network_comparison
6590.99 1629 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 6158.32 1.07026
6591.53 1626 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 6157.13 1.07055
6595.35 909 kinesin family member c3. [refseq;acc:nm_005550] 5995.49 1.10005
6597.55 1608 ubiquitin. [swissprot;acc:p02248] 6158.22 1.07134
6597.71 1416 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 6123.75 1.0774
6599.06 1317 orphan nuclear receptor tr2. [swissprot;acc:p13056] 6105.69 1.0808
6599.41 1316 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 6105.93 1.08082
6603.94 2534 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 6452.33 1.0235
2535 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
6606.21 1493 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 1.07482
6607.81 1309 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 6110.09 1.08146
6608.11 1679 proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] 6180.24 1.06923
6608.61 2637 protein kinase nyd-sp25. [refseq;acc:nm_033516] 6527.56 1.01242
6608.64 1945 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 6230.21 1.06074
1946 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
1948 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]
1949 ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
6610.46 1506 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] 6152.78 1.07439
1507 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
1508 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
6613.15 1631 brachyury protein (t protein). [swissprot;acc:o15178] 6179.59 1.07016
1632 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]
6613.46 1847 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 6215.55 1.06402
6617.91 1604 malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 1.07141
1605 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483]
6632.24 1336 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 6140.18 1.08014
6634.31 2508 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 6469.44 1.02548
6637.44 1537 evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] 6184.27 1.07328
6640.77 1347 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 6153.36 1.07921
1348 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
1349 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
6640.78 1402 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 6160.06 1.07804
6647.42 2319 putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 6362.48 1.04478
2320 t54 protein. [swissprot;acc:q92917]
6649.22 1036 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 6077.65 1.09404
6652.85 1920 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 6262.66 1.0623
1921 salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]
6653.52 1033 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 6080.91 1.09417
6655.11 811 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 6000.07 1.10917
6655.12 1612 eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 6212.98 1.07116
6655.9 2434 wd repeat domain 26. [refseq;acc:nm_025160] 6423.46 1.03619
6656.34 1489 vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] 6192.38 1.07492
6657.98 2198 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] 6344.31 1.04944
2199 sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
6659.39 1578 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] 6213.27 1.0718
6665.83 1610 eif-5a2 protein. [refseq;acc:nm_020390] 6222.4 1.07126
6666.87 2269 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] 6373.94 1.04596
6667.06 2273 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] 6374.64 1.04587
6668.72 1849 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 6267.93 1.06394
6670.1 2081 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] 6318.3 1.05568

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/