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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4414 to 4463 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
2207 SAP30 sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Divided 199.129 200.413 1.00645
2208 AP2M1 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]
P4HA1 prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Subtracted 209.54 208.162 1.378
2209 ABCC10 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Divided 199.129 200.413 1.00645
PROX1 homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Subtracted 209.54 208.162 1.378
2210 MAN2B1 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] Divided 199.129 200.413 1.00645
RAD1 rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Subtracted 209.54 208.162 1.378
2211 BRD2 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96 224.338
RRN3 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Divided 199.129 200.413 1.00645
2212 MRPS16 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 224.411 225.854 1.00643
P4HA2 prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Subtracted 209.54 208.162 1.378
2213 DHDH dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Divided 210.127 211.475 1.00642
MRPL18 mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Subtracted 223.58 224.943 1.363
2214 FABP4 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Divided 221.509 220.108 1.00637
VAMP2 vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Subtracted 200.063 198.71 1.353
2215 no value 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
RAPSN 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] Subtracted 215.547 214.194 1.353
2216 FABP7 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Divided 221.509 220.108 1.00637
VAMP1 vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Subtracted 200.063 198.71 1.353
2217 VAMP4 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]
WDR4 wd-repeat protein 4. [swissprot;acc:p57081] Divided 221.509 220.108 1.00637
2218 CDIPT 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
PMP2 myelin p2 protein. [swissprot;acc:p02689] Divided 221.509 220.108 1.00637
2219 ARFGAP1 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
KLHL8 kelch-like protein 8. [swissprot;acc:q9p2g9] Divided 221.509 220.108 1.00637
2220 PNMT phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
VAMP3 vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Subtracted 200.063 198.71 1.353
2221 no value beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 221.509 220.108 1.00637
DHDH dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Subtracted 210.127 211.475 1.348
2222 BCMO1 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Divided 221.509 220.108 1.00637
FDXR 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 FABP3 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
KIF3C kinesin-like protein kif3c. [swissprot;acc:o14782] Subtracted 219.045 220.377 1.332
2224 KIF3B kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 219.047 220.371 1.324
RPE65 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 INMT indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]
SIAH2 seven in absentia homolog 2. [refseq;acc:nm_005067] Subtracted 223.546 224.869 1.323
2226 no value 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] 177.515 178.831 1.316
CFL1 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Divided 217.955 219.336 1.00634
2227 ALAD delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Subtracted 217.185 218.498 1.313
CFL2 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Divided 217.955 219.336 1.00634
2228 CDC37 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 223.888 225.191 1.303
FDXR 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 no value 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
DSTN destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Divided 217.955 219.336 1.00634
2230 SAP30 sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Subtracted 199.129 200.413 1.284
UFD1L ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Divided 217.955 219.336 1.00634
2231 AP2M1 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
SYVN1 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Divided 221.842 223.246 1.00633
2232 ABCC10 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Subtracted 199.129 200.413 1.284

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
- Hugo is the HGNC identifier if it exists
- 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/