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