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 Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2180 to 2229 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1090 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
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 220.291 226.584 1.02857
1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 235.974 1.02847
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 210.722 205.826 1.02379
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 229.441 235.972 1.02846
1104 frizzled 8 precursor (frizzled-8) (fz-8) (hfz8). [swissprot;acc:q9h461] Low confidence 206.584 201.786 1.02378
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] High confidence 231.922 238.486 1.0283
1105 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 185.882 1.02828
tribbles homolog 2. [refseq;acc:nm_021643] Low confidence 203.515 198.787 1.02378
1106 mitochondrial carrier protein mgc4399. [refseq;acc:nm_032315] 201.02 196.352 1.02377
pxr2b protein. [refseq;acc:nm_016559] High confidence 212.945 207.109 1.02818
1107 rh type c glycoprotein. [refseq;acc:nm_016321] Low confidence 201.221 196.55 1.02376
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 204.603 210.324 1.02796
1108 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 1.02775
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 204.27 199.529 1.02376
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] 200.443 195.793 1.02375
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] High confidence 218.098 212.209 1.02775
1110 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 1.02769
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Low confidence 201.984 197.299 1.02375
1111 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] High confidence 217.99 212.123 1.02766
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 202.004 197.323 1.02372
1112 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] High confidence 251.863 258.829 1.02766
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 204.256 199.524 1.02372
1113 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 200.326 195.686 1.02371
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] High confidence 251.863 258.829 1.02766
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 200.679 196.033 1.0237
1115 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] High confidence 251.863 258.829 1.02766

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/