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 2151 to 2200 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1076 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] High confidence 174.387 179.697 1.03045
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Low confidence 206.757 201.939 1.02386
1077 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] High confidence 174.387 179.697 1.03045
frizzled 5 precursor (frizzled-5) (fz-5) (hfz5) (fze5). [swissprot;acc:q13467] Low confidence 206.587 201.773 1.02386
1078 er lumen protein retaining receptor 2 (kdel receptor 2) (elp-1). [swissprot;acc:p33947] 202.92 198.191
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] High confidence 174.387 179.697 1.03045
1079 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
er lumen protein retaining receptor 1 (kdel receptor 1). [swissprot;acc:p24390] Low confidence 202.92 198.191 1.02386
1080 brain protein 44-like protein (hspc040) (cgi-129) (pnas-115). [swissprot;acc:q9y5u8] 196.378 191.803 1.02385
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] High confidence 269.896 278.093 1.03037
1081 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 216.875 1.03027
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Low confidence 202.98 198.253 1.02384
1082 histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 203.804 199.058
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] High confidence 220.118 213.685 1.03011
1083 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]
protein p25-beta. [swissprot;acc:p59282] Low confidence 203.939 199.193 1.02383
1084 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] High confidence 220.118 213.685 1.03011
elovl family member 6, elongation of long chain fatty acids (fen1/elo2, sur4/elo3-like, yeast); long-chain fatty-acyl elongase. [refseq;acc:nm_024090] Low confidence 200.38 195.716 1.02383
1085 25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] 203.933 199.188 1.02382
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] High confidence 231.007 237.864 1.02968
1086 protein cgi-38. [swissprot;acc:q9bw30] Low confidence 203.9 199.157 1.02382
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] High confidence 236.679 243.679 1.02958
1087 cab2. [refseq;acc:nm_033419] Low confidence 200.375 195.715 1.02381
zinc finger protein 277. [swissprot;acc:q9nrm2] High confidence 236.679 243.679 1.02958
1088 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 219.673 213.378 1.0295
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Low confidence 203.333 198.607 1.0238
1089 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] High confidence 121.428 125.004 1.02945
neuronal cell death inducible putative kinase (skip3). [swissprot;acc:q96ru7] Low confidence 203.522 198.791 1.0238
1090 g-protein-coupled receptor induced protein. [refseq;acc:nm_025195] 203.52 198.79 1.02379
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] High confidence 226.218 232.88 1.02945
1091 block 23. [sptrembl;acc:q8nhw5] 226.205 232.858 1.02941
carnitine palmitoyltransferase i related c. [refseq;acc:nm_152359] Low confidence 203.519 198.789 1.02379
1092 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] High confidence 226.203 232.855 1.02941
ephrin type-b receptor 1 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eph-2) (net) (hek6) (elk). [swissprot;acc:p54762] Low confidence 210.722 205.826 1.02379
1093 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] High confidence 177.432 182.647 1.02939
ephrin type-a receptor 5 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor ehk-1) (eph homology kinase-1) (receptor protein- tyrosine kinase hek7). [swissprot;acc:p54756] Low confidence 210.722 205.826 1.02379
1094 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] High confidence 219.655 213.385 1.02938
ephrin type-a receptor 2 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eck) (epithelial cell kinase). [swissprot;acc:p29317] Low confidence 210.722 205.826 1.02379
1095 high-affinity cationic amino acid transporter-1 (cat-1) (cat1) (system y+ basic amino acid transporter) (ecotropic retroviral leukemia receptor homolog) (err) (ecotropic retrovirus receptor homolog). [swissprot;acc:p30825] 200.661 195.999
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] High confidence 213.552 207.463 1.02935
1096 ephrin type-a receptor 7 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor ehk-3) (eph homology kinase-3) (receptor protein- tyrosine kinase hek11). [swissprot;acc:q15375] Low confidence 210.722 205.826 1.02379
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] High confidence 212.345 206.339 1.02911
1097 ephrin type-b receptor 2 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eph-3) (drt) (receptor protein-tyrosine kinase hek5) (erk). [swissprot;acc:p29323] Low confidence 210.722 205.826 1.02379
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] High confidence 209.123 203.208 1.02911
1098 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 217.323 211.185 1.02906
ephrin type-a receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor sek) (receptor protein-tyrosine kinase hek8). [swissprot;acc:p54764] Low confidence 210.722 205.826 1.02379
1099 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] High confidence 217.315 211.183 1.02904
carnitine o-palmitoyltransferase i, mitochondrial liver isoform (ec 2.3.1.21) (cpt i) (cpti-l). [swissprot;acc:p50416] Low confidence 203.519 198.789 1.02379
1100 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] High confidence 209.052 203.183 1.02889
ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] Low confidence 210.722 205.826 1.02379

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/