GlyClass

GlycoEnzDB
Comprehensive glycoEnzyme database and dynamic pathway generation

Description: The GlycoEnzDB is a manually curated glycoEnzyme database, primarily focused on humans. It covers 390 enzymes across 28 pathway maps. Facilities are also available to create custom glycosylation reaction pathways using experimental data in SBML format and for pathway simulation
Contacts: Sriram Neelamegham (neel@buffalo.edu), Yusen Zhou (yusenzho@buffalo.edu) or Ted Groth (tgroth@buffalo.edu).

GlycoEnzDB
Create glycosylation pathway
Custom database generation
Instructions/Reference
 

Pathway Map

PMM2



General Information
Gene Symbol:   
PMM2
Protein name:   
Phosphomannomutase 2
Enzyme Class:   
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   

Man(1P) or Man(6P) Man(6P) or Man(1P)
Reaction (IUBMB):   
No specified reaction.

About

• Phosphomannomutase 1 transfers a phosphate group from the 1 carbon to the 6 carbon on mannose 1 phosphate.
• PMM1 and 2 share 65% homology.
• PMM2 deficiency is recognized as a congenital disease of glycosylation. The lack of available phosphorylated mannose decreases due to the lack of activity and causes underglycosylation. The disease causes a wide array of deformities and metabolic disorders.


Related Pathway
KEGG ORTHOLOGY:   
KEGG Pathway:   
Reactome:   

Related Database
Organism:   
Homo sapiens
Uniprot:   
NCBI GeneID:   
GlyMap GeneID:   
DNA aRefSeq:   
Protein RefSeq:   
BRENDA:   
OMIM number:   
GeneCards database:   

Enzyme Specificity
Glycan Type:  
     
Compartment:  
     
Substrate:  
     Man(1P) or Man(6P)
Product:  
     Man(6P) or Man(1P)
Constraints:  
     None

Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:       (pmol/cell • hr)       KM:       (pM)
Relative conc of enzymes in compartment.(sum will be normalized to 1)
ER Cis- Medial- Trans- TGN











Expression Data in Tissue {ref. 5} Source from NCBI gene database
adrenal appendix bone marrow brain colon duodenum endometrium esophagus fat gall bladder heart kidney liver lung lymph node ovary pancreas placenta prostate salivary gland skin small intestine spleen stomach testis thyroid urinary bladder 30 20 10 0 RPKM
Expression Data in Cells {ref. 13} Source from Cancer Cell Line Encyclopedia database
Kidney Lung Breast Prostate Large intestine Ovary HL60 haematopoietic and lymphoid tissue Skin Central nervous system 786O A498 ACHN CAKI1 UO31 A549 EKVX HOP62 HOP92 NCIH226 NCIH23 NCIH322 NCIH460 NCIH522 SHP77 BT549 HS578T MCF7 MDAMB231 MDAMB468 T47D DU145 PC3 HCT116 HCT15 HT29 KM12 SW620 OVCAR4 OVCAR8 IGROV1 SKOV3 HL60 K562 RPMI8226 LOXIMVI MALME3M RPMI7951 SKMEL28 SKMEL5 UACC257 UACC62 SF268 SF295 SF539 SNB75 100 80 60 40 20 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000268261 ENST00000565221 ENST00000566540 ENST00000567697 ASCL1


miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-718 295-302 -0.724 99.0 -0.724 99.0 noncon
hsa-miR-6084 294-301 -0.72 99.0 -0.72 99.0 noncon
hsa-miR-1471 829-836 -0.685 99.0 -0.515 98.0 noncon
hsa-miR-6805-5p 248-255 -0.627 99.0 -0.627 99.0 noncon
hsa-miR-6784-5p 1358-1365 -0.531 98.0 -0.405 96.0 noncon
hsa-miR-6508-3p 199-206 -0.526 99.0 -0.526 99.0 noncon
hsa-miR-3656 91-98 -0.514 98.0 -0.514 98.0 noncon
hsa-miR-5091 722-729 -0.508 97.0 -0.388 96.0 noncon
hsa-miR-5580-5p 35-42 -0.47 98.0 -0.47 99.0 noncon
hsa-miR-7110-5p 240-247 -0.462 95.0 -0.462 96.0 noncon
hsa-miR-3972 773-780 -0.434 98.0 -0.334 98.0 noncon
hsa-miR-6842-5p 240-247 -0.43 93.0 -0.43 95.0 noncon
hsa-miR-3135a 100-107 -0.421 97.0 -0.421 98.0 noncon
hsa-miR-1909-3p 399-406 -0.416 98.0 -0.32 96.0 noncon
hsa-miR-5571-3p 1120-1127 -0.405 99.0 -0.312 98.0 noncon
hsa-miR-6766-5p 234-241 -0.405 97.0 -0.405 97.0 noncon
hsa-miR-6756-5p 234-241 -0.394 96.0 -0.394 97.0 noncon
hsa-miR-7974 1411-1418 -0.394 97.0 -0.304 95.0 noncon
hsa-miR-4505 1329-1336 -0.393 98.0 -0.303 96.0 noncon
hsa-miR-503-3p 260-267 -0.39 97.0 -0.39 98.0 noncon
hsa-miR-6794-5p 249-255 -0.389 97.0 -0.389 98.0 noncon
hsa-miR-6851-5p 148-155 -0.385 97.0 -0.385 98.0 noncon
hsa-miR-6515-5p 1317-1324 -0.382 98.0 -0.295 96.0 noncon
hsa-miR-6846-5p 247-253 -0.378 94.0 -0.378 95.0 noncon
hsa-miR-6848-5p 247-253 -0.378 94.0 -0.378 95.0 noncon
hsa-miR-6776-5p 982-989 -0.373 98.0 -0.288 97.0 noncon
hsa-miR-1249-5p 1316-1323 -0.373 98.0 -0.288 96.0 noncon
hsa-miR-6797-5p 1316-1323 -0.373 98.0 -0.288 96.0 noncon
hsa-miR-6722-3p 399-406 -0.371 97.0 -0.287 95.0 noncon
hsa-miR-1299 167-174 -0.37 98.0 -0.37 99.0 noncon
hsa-miR-7108-3p 15-21 -0.369 94.0 -0.369 95.0 noncon
hsa-miR-6837-3p 1466-1473 -0.368 98.0 -0.284 97.0 noncon
hsa-miR-5001-5p 1275-1282 -0.363 96.0 -0.281 93.0 noncon
hsa-miR-6752-5p 240-247 -0.362 93.0 -0.362 94.0 noncon
hsa-miR-4498 1275-1282 -0.361 96.0 -0.279 93.0 noncon
hsa-miR-6766-5p 264-270 -0.356 95.0 -0.356 96.0 noncon
hsa-miR-6735-3p 446-453 -0.355 98.0 -0.275 97.0 noncon
hsa-miR-6799-5p 1325-1332 -0.354 99.0 -0.274 99.0 noncon
hsa-miR-6756-5p 264-270 -0.349 94.0 -0.349 95.0 noncon
hsa-miR-4417 1277-1284 -0.345 97.0 -0.267 96.0 noncon
hsa-miR-1324 1350-1357 -0.343 98.0 -0.266 98.0 noncon
hsa-miR-939-3p 468-475 -0.34 97.0 -0.263 96.0 noncon
hsa-miR-5787 1329-1336 -0.339 98.0 -0.263 97.0 noncon
hsa-miR-4725-3p 230-237 -0.338 96.0 -0.338 97.0 noncon
hsa-miR-5001-5p 465-472 -0.334 94.0 -0.259 92.0 noncon
hsa-miR-4261 1497-1503 -0.334 98.0 -0.079 78.0 noncon
hsa-miR-4498 465-472 -0.332 94.0 -0.257 91.0 noncon
hsa-miR-4758-3p 541-548 -0.33 96.0 -0.256 95.0 noncon
hsa-miR-4493 976-983 -0.33 96.0 -0.256 95.0 noncon
hsa-miR-6741-3p 60-67 -0.33 96.0 -0.33 97.0 noncon
hsa-miR-6875-5p 1033-1040 -0.323 97.0 -0.25 95.0 noncon
hsa-miR-492 812-819 -0.322 94.0 -0.25 92.0 noncon
hsa-miR-6780b-5p 230-237 -0.322 95.0 -0.322 96.0 noncon
hsa-miR-1202 773-780 -0.313 98.0 -0.243 97.0 noncon
hsa-miR-493-3p 1456-1462 -0.313 96.0 -0.243 95.0 noncon
hsa-miR-3667-3p 174-181 -0.312 97.0 -0.312 97.0 noncon
hsa-miR-6802-3p 1372-1379 -0.311 94.0 -0.241 93.0 noncon
hsa-miR-6769b-5p 263-269 -0.309 97.0 -0.309 97.0 noncon
hsa-miR-874-5p 1235-1242 -0.308 93.0 -0.239 90.0 noncon
hsa-miR-1233-5p 73-80 -0.308 94.0 -0.308 95.0 noncon
hsa-miR-3689d 148-155 -0.307 97.0 -0.307 98.0 noncon
hsa-miR-298 1051-1058 -0.305 97.0 -0.237 96.0 noncon
hsa-miR-5681b 408-415 -0.303 97.0 -0.235 96.0 noncon
hsa-miR-125b-5p 907-914 -0.303 95.0 -0.235 94.0 con
hsa-miR-3126-5p 1033-1040 -0.299 96.0 -0.232 95.0 noncon
hsa-miR-6769a-5p 263-269 -0.299 96.0 -0.299 97.0 noncon
hsa-miR-6762-3p 1380-1387 -0.298 95.0 -0.232 93.0 noncon
hsa-miR-4283 1356-1362 -0.297 93.0 -0.231 91.0 noncon
hsa-miR-125a-5p 907-914 -0.295 95.0 -0.229 93.0 con
hsa-miR-6778-5p 73-80 -0.292 93.0 -0.292 95.0 noncon
hsa-miR-4761-5p 521-528 -0.291 97.0 -0.226 95.0 noncon
hsa-miR-4726-5p 200-206 -0.29 91.0 -0.29 93.0 noncon
hsa-miR-4319 907-914 -0.287 95.0 -0.223 93.0 con
hsa-miR-4271 230-237 -0.286 96.0 -0.286 97.0 noncon
hsa-miR-4487 1385-1392 -0.283 95.0 -0.22 93.0 noncon
hsa-miR-1237-3p 170-177 -0.281 97.0 -0.281 98.0 noncon
hsa-miR-3937 509-515 -0.28 93.0 -0.218 91.0 noncon
hsa-miR-4734 93-99 -0.279 91.0 -0.279 93.0 noncon
hsa-miR-4505 926-933 -0.279 94.0 -0.217 92.0 noncon
hsa-miR-762 1275-1282 -0.277 95.0 -0.216 93.0 noncon
hsa-miR-4492 1275-1282 -0.277 95.0 -0.216 94.0 noncon
hsa-miR-637 242-248 -0.277 94.0 -0.277 96.0 noncon
hsa-miR-24-3p 1163-1170 -0.272 96.0 -0.212 94.0 noncon
hsa-miR-4792 84-90 -0.271 94.0 -0.271 95.0 noncon
hsa-miR-6748-3p 444-450 -0.269 93.0 -0.209 91.0 noncon
hsa-miR-144-3p 1446-1453 -0.267 97.0 -0.208 96.0 con
hsa-miR-7974 1281-1288 -0.265 91.0 -0.206 88.0 noncon
hsa-miR-2110 304-310 -0.265 96.0 -0.265 97.0 noncon
hsa-miR-665 492-499 -0.264 96.0 -0.206 95.0 noncon
hsa-miR-371b-3p 1214-1220 -0.263 92.0 -0.205 91.0 noncon
hsa-miR-604 95-101 -0.263 96.0 -0.263 96.0 noncon
hsa-miR-4755-3p 706-712 -0.261 93.0 -0.203 92.0 noncon
hsa-miR-4492 465-472 -0.256 94.0 -0.2 93.0 noncon
hsa-miR-3157-3p 43-49 -0.256 95.0 -0.256 97.0 noncon
hsa-miR-4645-5p 342-349 -0.251 96.0 -0.218 96.0 noncon
hsa-miR-3156-3p 740-747 -0.25 94.0 -0.195 93.0 noncon
hsa-miR-5580-5p 1383-1389 -0.25 91.0 -0.195 89.0 noncon