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 Value Type description Filtered Network Comparison Type Interaction Map green network_comparison red
Results: HTML CSV LaTeX Showing element 2180 to 2229 of 8289 in total
Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided
Rank
description
Interaction Map
green
network_comparison
red
1090 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] High confidence 232.88 1.02945 226.218
1091 block 23. [sptrembl;acc:q8nhw5] 232.858 1.02941 226.205
carnitine palmitoyltransferase i related c. [refseq;acc:nm_152359] Low confidence 198.789 1.02379 203.519
1092 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] High confidence 232.855 1.02941 226.203
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 205.826 1.02379 210.722
1093 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] High confidence 182.647 1.02939 177.432
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 205.826 1.02379 210.722
1094 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] High confidence 213.385 1.02938 219.655
ephrin type-a receptor 2 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eck) (epithelial cell kinase). [swissprot;acc:p29317] Low confidence 205.826 1.02379 210.722
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] 195.999 200.661
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] High confidence 207.463 1.02935 213.552
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 205.826 1.02379 210.722
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 206.339 1.02911 212.345
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 205.826 1.02379 210.722
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] High confidence 203.208 1.02911 209.123
1098 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 211.185 1.02906 217.323
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 205.826 1.02379 210.722
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 211.183 1.02904 217.315
carnitine o-palmitoyltransferase i, mitochondrial liver isoform (ec 2.3.1.21) (cpt i) (cpti-l). [swissprot;acc:p50416] Low confidence 198.789 1.02379 203.519
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 203.183 1.02889 209.052
ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] Low confidence 205.826 1.02379 210.722
1101 ephrin type-b receptor 6 precursor (tyrosine-protein kinase-defective receptor eph-6) (hep). [swissprot;acc:o15197]
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] High confidence 226.584 1.02857 220.291
1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 235.974 1.02847 229.442
ephrin type-a receptor 8 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eek) (eph-and elk-related kinase) (hek3). [swissprot;acc:p29322] Low confidence 205.826 1.02379 210.722
1103 ephrin type-a receptor 3 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor etk1) (hek) (hek4). [swissprot;acc:p29320]
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] High confidence 235.972 1.02846 229.441
1104 frizzled 8 precursor (frizzled-8) (fz-8) (hfz8). [swissprot;acc:q9h461] Low confidence 201.786 1.02378 206.584
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] High confidence 238.486 1.0283 231.922
1105 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 185.882 1.02828 191.139
tribbles homolog 2. [refseq;acc:nm_021643] Low confidence 198.787 1.02378 203.515
1106 mitochondrial carrier protein mgc4399. [refseq;acc:nm_032315] 196.352 1.02377 201.02
pxr2b protein. [refseq;acc:nm_016559] High confidence 207.109 1.02818 212.945
1107 rh type c glycoprotein. [refseq;acc:nm_016321] Low confidence 196.55 1.02376 201.221
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] High confidence 210.324 1.02796 204.603
1108 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 212.119 1.02775 218.006
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292] Low confidence 199.529 1.02376 204.27
1109 mitogen-activated protein kinase 13 (ec 2.7.1.37) (stress-activated protein kinase-4) (mitogen-activated protein kinase p38 delta) (map kinase p38 delta). [swissprot;acc:o15264] 195.793 1.02375 200.443
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] High confidence 212.209 1.02775 218.098
1110 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 222.782 1.02769 216.78
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Low confidence 197.299 1.02375 201.984
1111 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] High confidence 212.123 1.02766 217.99
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Low confidence 197.323 1.02372 202.004
1112 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] High confidence 258.829 1.02766 251.863
vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0] Low confidence 199.524 1.02372 204.256
1113 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 195.686 1.02371 200.326
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] High confidence 258.829 1.02766 251.863
1114 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
solute carrier family 7 (cationic amino acid transporter, y+ system), member 3. [refseq;acc:nm_032803] Low confidence 196.033 1.0237 200.679
1115 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] High confidence 258.829 1.02766 251.863

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/