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 4427 to 4476 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2214 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Divided 221.509 220.108 1.00637
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Subtracted 200.063 198.71 1.353
2215 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 215.547 214.194
fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Divided 221.509 220.108 1.00637
2216 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Subtracted 200.063 198.71 1.353
2217 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]
wd-repeat protein 4. [swissprot;acc:p57081] Divided 221.509 220.108 1.00637
2218 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Subtracted 200.063 198.71 1.353
myelin p2 protein. [swissprot;acc:p02689] Divided 221.509 220.108 1.00637
2219 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Subtracted 200.063 198.71 1.353
kelch-like protein 8. [swissprot;acc:q9p2g9] Divided 221.509 220.108 1.00637
2220 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Subtracted 200.063 198.71 1.353
2221 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 221.509 220.108 1.00637
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Subtracted 210.127 211.475 1.348
2222 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Divided 221.509 220.108 1.00637
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Subtracted 211.81 213.153 1.343
2223 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Divided 221.509 220.108 1.00637
kinesin-like protein kif3c. [swissprot;acc:o14782] Subtracted 219.045 220.377 1.332
2224 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 219.047 220.371 1.324
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Divided 221.509 220.108 1.00637
2225 indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]
seven in absentia homolog 2. [refseq;acc:nm_005067] Subtracted 223.546 224.869 1.323
2226 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Divided 217.955 219.336 1.00634
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 177.515 178.831 1.316
2227 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Divided 217.955 219.336 1.00634
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Subtracted 217.185 218.498 1.313
2228 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 223.888 225.191 1.303
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Divided 211.81 213.153 1.00634
2229 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Subtracted 199.129 200.413 1.284
destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Divided 217.955 219.336 1.00634
2230 sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Subtracted 199.129 200.413 1.284
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Divided 217.955 219.336 1.00634
2231 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Subtracted 199.129 200.413 1.284
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Divided 221.842 223.246 1.00633
2232 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 215.547 214.194 1.00632
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Subtracted 199.129 200.413 1.284
2233 lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] Divided 202.414 203.691 1.00631
2234 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Subtracted 199.129 200.413 1.284
seven in absentia homolog 1. [refseq;acc:nm_003031] Divided 223.608 225.005 1.00625
2235 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 200.95 199.711 1.0062
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Subtracted 196.748 195.466 1.282
2236 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 209.197 207.915
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 222.959 224.337 1.00618
2237 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 222.965 224.343
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Subtracted 209.197 207.915 1.282
2238 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Divided 222.959 224.337 1.00618
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Subtracted 209.197 207.915 1.282

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/