EpoDB Controlled Vocabularies

New names (from the 2.2 update): ========== name : gene family name(s) acetylcholinesterase : carboxylesterase, membrane protein acyl-CoA dehydrogenase, very-long-chain specific : membrane protein, mitochondrial protein alpha-globin : globin, 'globin, alpha-like' galactokinase 1 : galactose metabolism histone H3l : histone, nuclear protein histone H3r : histone, nuclear protein histone H1.4 : histone, nuclear protein MafB : bZip protein, transcription factor, nuclear protein Na/K-transporting ATPase beta-2 : membrane protein, ATPase Gene name: ========== 15-lipoxygenase beta-actin beta-actin1 beta-actin2 gamma-actin adenosine deaminase adenylate kinase band 3 protein band 4.2 Duffy antigen/chemokine receptor elongation factor-1 alpha erythropoietin erythropoietin receptor EKLF ferritin heavy chain ferritin light chain c-fos galactosephosphate uridylyltransferase A alpha-globin B alpha-globin C alpha-globin I alpha-globin II alpha-globin alpha 1-globin alpha 2-globin alpha A-globin alpha A I-globin alpha A II-globin alpha D-globin beta A-globin beta A I-globin beta A II-globin beta B-globin beta C-globin beta F-globin beta-globin beta-globin, major beta-globin, minor beta h 0-globin beta h 1-globin beta L I-globin delta-globin epsilon 2-globin epsilon 4-globin epsilon-globin epsilon I-globin epsilon II-globin epsilon III-globin epsilon IV-globin epsilon V-globin epsilon VI-globin epsilon y-globin A gamma-globin G gamma-globin gamma-globin pi-globin psi 1-globin psi alpha 1-globin psi beta-globin psi beta I-globin psi beta II-globin psi zeta 1-globin theta-globin zeta 1-globin zeta 2-globin zeta-globin GM-CSF glucose-6-phosphate dehydrogenase glutathione-S-transferase-pi histone H1D histone H2A histone H3 histone H3-IV histone H3-V histone H5 histone H5A histone H5B HOX-1A HOX-1C HOX-2A HOX-2B HOX-3D hsp70.1 hypoxanthine phosphoribosyltransferase IL-3 c-jun junD lactate dehydrogenase-A max c-myc porphobilinogen deaminase pyruvate kinase, L-type c-Ha-ras-1 retinoblastoma ribonucleotide reductase, M2 subunit ribosomal protein L9 TAFII30 SCL Mn superoxide dismutase MafB#'bZip protein','transcription factor', 'nuclear protein' Na/K-transporting ATPase beta-2#'membrane protein',ATPase triosephosphate isomerase uroporphyrinogen decarboxylasezeta 2-globin
Gene family (Protein function) name: ==================================== ATPase carboxylesterase cytoskeletal protein actin dioxygenase globin globin, alpha-like globin, beta-like galactose metabolism glycolytic enzyme growth factor heme biosynthesis porphyrin biosynthesis hexose monophosphate enzyme iron transport protein ferritin membrane protein chemokine receptor mitochondrial protein nuclear protein histone transcription factor TBP-associated factor zinc finger protein helix-loop-helix protein homeobox protein bZip protein nucleoside deaminase peptide elongation factor phosphotransferase protooncogene purine salvage radical scavenger ribosomal protein transferase tumor suppressor
Developmental Stage ========================== embryo human: up tp 5 wks post conception: Crown-rump-length (10mm, stage 14-15) fetal human: 6 wks post conception to birth: CRL =10mm (or greater) Stage 16 -17 prenatal postnatal neonatal adult egg larval tadpole embryo:3 days postnatal:10 weeks postnatal:8 to 12 weeks postnatal:8 weeks prenatal:19 to 20 weeks postnatal:3-7 days postnatal:5 days
Cell Type: ========= Primary cells: BFU-E BFU-E/Meg CFU-E CFU-GM basophils blast cells blood group A(HPA)+ cell eosinophils erythroblast erythroblast-like cells erythroblast: basophilic erythroblast: normoblasts erythrocyte erythrocyte: definitive erythroid cells erythroid cells: preleukemic fibroblast fibroblast:3T3 fibroblast:skin granulocyte: metamyelocyte granulocyte: myelocyte granulocytes leukemic cells leukocytes lymphocytes macrophages mast cells megakaryoblasts megakaryocytes monocytes mononuclear cells myeloid cells myeloid tumor cells neutrophils nonerythroid cells:TER119- platelets primordial germ cells reticulocyte erythrocyte Cell lines: 32D:CL23 (myeloid cell line) 32D:c13 416B (myeloid cell line) 6- (mast cell line) 99.4 Mst (mast cell line) BV-173 CCRF-CEM CMK CML-T1 Cess DU.528 Dami Daudi E-Cadherin+ cells EM2 EML ES cell line:D3 FDCP1 (myeloid cell line) FL37 (mast cell line) Fmp 1.6 (mast cell line) HC3 (mast cell line) HD3 HEL HL60 HSB2 J2E J774 (myeloid cell line) Jurkat K562 KG-1 KG-1a KU.812 Km3 M 1 (myeloid cell line) MCF-7 MEL MO7e MOLM-1 MOLT-4 MPC-11 MPRO Meg-01 NFS60 (myeloid cell line) Nalm-1 Nalm-6 OCI/AML-4 P815 (mast cell line) PU-5 (myeloid cell line) Raji Reh SAM-1 SKW3 SP2 SPI-801 T-lymphocytic cell line:MSB-1 TF-1 TFP10 TMM U266 UT-7 WEHI:265 (myeloid cell line) WEHI:274 (myeloid cell line) heterokaryons:K562 x ES heterokaryons:MEL x K562 histiocytic cell line:U937 lymphoid cell line:AHR 77 lymphoid cell line:Priess lymphoid cell line:T51 monocytic cell line:JOSK-I monocytic cell line:JOSK-K monocytic cell line:JOSK-S monocytic cell line:THP-1 murine teratocarcinoma cells myeloid cell line:Eol-3 myeloid cell line:Kasumi-1 myeloid cell line:ML-1
Tissue Type: ============ bone marrow brain colon cord blood embryo embryo:anterio half embryo:anterio half:zona opaca embryo:anterio half:zona pellucida embryo:posterio half embryo:posterio half:zona opaca embryo:posterio half:zona pellucida heart kidney liver lung lymph node muscle ovary pancreas peripheral blood placenta prostate red pulp skeletal muscle small intestine spleen stomach testis thymus white pulp yolk sac human: 5 week embryos embryo:zona opaca embryo:zona pellucida retina gut skin neuroepithelium:cortical layer neuroepithelium:ventricular layer gonads
Type of Experiment: ================== FACS FACS: double immunofluorescence with antibodies FACS: flow cytometric analysis FISH Northern RNase protection RNase protection: S1 RT-PCR Southern blot Western (immunoblot) binding with I125-labeled ligand gel electrophoresis: native gel retardation, move-ups) immunoprecipitation: Western immunoprecipitation: electrophoresis immunoprecipitation: filter in situ hybridization nuclear run-off trancription analysis nuclear run-on transcription analysis protein synthesis: globin chain synthesis slot blot analysis
Factors Added ============= G-CSF GM-CSF IGF-1 (insulin-like growth factor-1) IL-2 IL-3 IL-4 IL-6 IL-9 LIF (leukemia inhibitory factor) M-CSF MGF (mast cell growth factor) RA (retinoic acid) chemical: Am80 (4-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenylcarbamoyl)-benzoic acid) chemical: TPA chemical:8-(p-chlorophenylthio)-cGMP chemical:8-bromo-cGMP chemical:AZT (zidovudine) chemical:DMSO (dimethyl sulfoxide) chemical:FeSIH (iron salicylaldehyde isonicotinoylhydrazone) chemical:GS-NO (S-nitrosoglutathione) chemical:HMBA chemical:SIN chemical:SNP chemical:TPA (12-O-tetradecanoylphorbol-13-acetate) chemical:delta-ALA chemical:desferrioxamine chemical:diosgenin chemical:hemin chemical:phenylhydrazine chemical:phorbol-12,13-dibutyrate chemical:sangivamycin (nucleoside analogue) chemical:sodium butyrate chemical:staurosporine (microbal alkaloid) erythropoietin heat insulin kit ligand (stem cell factor) oligodeoxynucleotides:p53 antisense oligodeoxynucleotides:p53 sense oligodeoxynucleotides:retinoblastoma antisense oligodeoxynucleotides:retinoblastoma sense protein kinase inhibitor:H7 protein kinase inhibitor:H8 retinoic acid serum: FCS vitamin D3