Glossary
Ab
Antibody
a handle used to describe a protein identified by an antibody
AcAb
an antibody that detects a specific acetylation site when it is acetylated
a detection method used in an acetylation assay
a handle used to describe a protein identified by an antibody to a specific acetylation site
acetyl
acetylation
a modification used to represent acetylation
act
activated; used when a protein has been shown experimentally to be capable of catalyzing a reaction
a modification used to represent activation
agarose
a handle used to describe a protein or chemical immoblized on agarose
AminoAcids
molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids.
a Treatment used when mixtures of amino acids are added to cells
AS-DNA
antisense DNA
AS-RNA
antisense RNA
auto
used when the substrate of a kinase reaction is the kinase itself
B-DNA
DNA in the B conformation
represented by Poly(dA-dT)-Poly(dT-dA)  17618271(M)  16785313(M)
the right-handed typical form of double helix DNA in which the chains twist up and to the right around the front of the axis of the helix and that has usually ten base pairs in each helical turn and two grooves on the external surface [Merriam-Webster Dictionary]
BeadArray
an ELISA performed on suspended beads and analysed by FACS
a detection method used in a secretion assay
bGal
beta-Galactosidase Enzyme assay
sample containing bGal is incubated with colorless substrate ONPG (o-nitrophenyl-beta-D-galactopyranoside).  Active enzyme hydrolyzes subtrate to o-nitrophenyl which is yellow.  The reaction is terminated with sodium carbonate and the absorbance at 420 nM is measured by spectrophotometry. [Promega catalog]
BiFC
bimolecular fluorescence complementation
A method of viewing the association of proteins inside living cells.  The intact Green fluorescent protein (and its variants CFP, YFP, BFP, and RFP) is fluorescent. However, when the fluorescent protein is split into N and C-terminal halves, the molecule does not produce fluorescence. Fusing of each of the two non-fluorescent fragments to two putative interacting partners leads to restoration of fluorescence within a cell by reconstituting the split fluorophore. This fluorescence is detected via fluorescence microscopy, which can be recorded by a mounted camera. The advantage of the BiFC method over other methods of visualizing protein-protein interactions is that it gives an indication of interaction, as well as cellular localization of the complex. [Wiki]
biotin
a streptavidin binding protein used as a protein tag
a handle used to describe a protein or chemical prebound to biotin
biotin-labeling
a detection method used for detecting protein surface expression
a detection method used in a suface-exp assay
BMLS
Basal medium with low serum
same as BMS but serum concentration is <2%  (or significantly lower than that in growth medium)
BMS
Basal medium with serum
Basal medium contains balanced salt solutions, amino acid, vitamins
exampes: DMEM, MEM, RPMI
any growth factor supplements should be listed separately
Serum can be Fetal bovine serum, calf serum, newborn calf serum, horse serum
The concentration of serum is > 5%
BMS is used when the medium used during an experiment is not explicitly stated
BProtein
a single gene product
A BProtein uses its Pathway Logic name as declared in proteinops.maude
Any numbers used involving amino-acid sequence refer to the isoform chosen by UniProt as the 'canonical' sequence unless another splice variant is designated
BSS
Balanced Salt Solution
may contain Ca2+ or Mg2+
does not contain serum or amino acids
CA
constitutively active
CAAX
a residue located near the C-terminal end of Ras-family proteins
used in shorthand to describe a mutation - meaning that a CAAX box was added to protein to cause consitutive localization to membrane
an amino acid consensus sequence
C = cysteine to be prenylated
A = any aliphatic amino acid (leucine (L), isoleucine (I), or valine (V))
X = any amino acid
CAT
Chloramphenicol AcetylTransferase Assay
a detection method used in a Gal4-reporter assay
a detection method used in a LexA-reporter assay
a detection method used in a promo-reporter assay
a detection method used in a RE-reporter assay
CB
Commassie Blue stain
a handle used to describe a protein or chemical identified using Commassie Blue stain
Chemical
anything that is not a Protein or a Gene
ChIP
Chromatin ImmunoPrecipitation Assay
a detection method used in a boundto assay
CHX-WB
cyclohexamide treatment followed by western blot
a detection method used in a prot-stability assay
CIA
catalytically inactive
CIAP
Calf Intestine Alkaline Phosphatase
ClAb
an antibody that detects a the cleavage product of a Protein cleaved at a specific site
a detection method used in a cleavage assay
a handle used to identify a cleaved protein in a cleavage assay
CM
conditioned medium
Composite
a group of Proteins often referred to as one protein
examples: Ampk, PKA
Composite declarations can be found in proteinops.maude
coppts
coprecipitates
CrmA
a caspase inhibitor 14739303(C)
A serine-protease inhibitor encoded by cowpox virus 8034697(D)
the cowpox viral protein crmA that blocks caspase-8-induced apoptosis by physically interacting with and inhibiting processing of caspase-8 precursor (20). 10753878(C)
Crosstide
a peptide substrate (GRPRTSSFAEG) used for kinase assays
Ctxb
Cholera Toxin B-subunit used for visualizing GM1-gangliosides in lipid rafts
a handle used to identify Golga2
Cy3
a fluorophore used for labeling proteins
a handle used to identify proteins labeled with Cy3
Cy5
a fluorophore used for labeling proteins
a handle used to identify proteins labeled with Cy5
datum
an expression that describes an experiment using a formal grammar
DBD
DNA binding domain of a transcription factor
density-gradient
a size separation method using centrifugation through glycerol or sucrose gradients: a detection method
a detection method used in an oligomerization assay
dig
details in glossary - used when the mutations are too bulky to use in shorthand
details:
"K63-only"
Ubiq(K6R/K11R/K29R/K33R/K48R)
"K48-only"
Ubiq(K6R/K11R/K29R/K33R/K63R)
"no-lysines"
Ubiq(K6R/K11R/K27R/K29R/K33R/K48R/K63R)
DKO
double knockout
DRNAi
double interferring RNA
dsDNA
double stranded DNA
dsRNA
double stranded RNA
transcribed in vitro from PCR products using T7 RNA polymerase  16625202(M)
used in:  16785313
used as a ligand for TLR3
ELISA
Enzyme-Linked Immunosorbent Assay
a detection method used in a boundby assay
a detection method used in an oligo-binding assay
a detection method used in a prot-exp assay
a detection method used in a secretion assay
EM
Electron Microscopy
a detection method used in a colocwith assay
EMSA
Electrophoretic Mobility Shift Assay
a detection method used in an oligo-binding assay
FACS
Fluorescence Activated Cell Sorter
a detection method used in a prot-exp assay
a detection method used in a suface-exp assay
Family
a set of similar Proteins referred to by one name
A Family is used in rules and datums instead of a Protein when it is not possible to distinguish between the family members studied.
Family declarations can be found in proteinops.maude
FarWestern
a method used to determine the direct binding of a substance to a denatured protein.
a detection method used in a boundby assay
FasL-XL
crosslinked FasL
soluble FasL trimer cross-linked either chemically or with an anti-Tag Ab
required to induce apoptosis and cytotoxicity by FasL  12556501(D)
FBS
fetal bovine serum
Flag
a peptide tag used for identifying proteins
a handle used to identify or isolate proteins labeled with Flag
Fluor
Fluorescence
a handle used to identify proteins labeled with a fluorescent substance
FRET
Förster resonance energy transfer
a detection method used in a colocwith assay
a detection method used in a GTP-bdpg assay
Ft
any subspecies of Franciscella tularensis
Gal4-DBD
The DNA-binding domain of Gal4
a handle used to enable activated transcription factors to interact with a Gal4-reporter
GDPbS
guanosine 5'-[beta-thio]diphosphate
Gene
a string of nucleotides that codes for a Protein
Names of Genes in this model are derived from the Protein name (eg. the name of the gene for the protein Erk1 is Erk1-gene)
GMPPCP
used as a GTP analog by [16892055]
5'-guanylylmethylenebisphosphonate
GST
glutathione S-transferase
a handle used to describe or isolate a protein fused to GST
GTPgS
guanosine 5'-O-[gamma-thio]triphosphate
nonhydrolyzable G-protein-activating analog of GTP
handle
a Sort used in curation shorthand to describe the way a protein is identified in an experiment
HeJ-mut
TLR4 loss-of-function mutation in C3H/HeJ mice
HeterokaryonAssay
a method used to detect nuclear export
a detection method used in a nuc-export assay
His
a peptide tag containing multiple histidines used for identifying proteins
a handle used to identify or isolate proteins labeled with His
Hook
a Protein, Chemical, or nucleic acid used to "pull" Subject out of a lysate or reaction
HPLC
high performance liquid chromotography
HPLC-PAA-ED
High Performance Liquid Chromatograph followed by Phosphoamino Acid Analysis and Edman Degradation.
a detection method used in a phos assay
HRKnockdown
knockdown in a cell line by homologous recombination
ICP-AES
Inductively coupled plasma atomic emission spectroscopy
IHC
immunohistochemistry
a detection method used in a colocwith assay
a detection method used in an internalization assay
a detection method used in a locatedin assay
a detection method used in an oligomerization assay
InGelKinase
An activity assay performed on a kinase embedded in a polyacryamide gel.
a detection method used in an IVKA assay
IP
immunoprecipitate
The complex isolated from a lysate using an antibody against a protein or a protein-tag
IPfrom
the source of an immunoprecipite used in a test-tube experiment
irt
in response to
used when cells are treated with an external agent (addition of a reagent or application of a stress)
IVKA
in vitro kinase assay
an assay used to determine the ability of the complex immunoprecipitated with a protein to phosphorylate a substrate
IVnucImport
In Vitro Nuclear Import
an detection method used in a nuc-import assay
IVT
in vitro transcribed
k
a prefix used to designate a modified protein expressed from a knockin sequence driven by the endogenous promoter.
K48poly
a modification used for Ubiquitin polymerized via K48 linkages
K48poly
a modification used to for Ubiquitin polymerized via K63 linkages
K48poly
a modification used to describe a protein bound to Ubiquitin polymerized via K63 linkages
K48ubiq
a modification used to describe a protein bound to Ubiquitin polymerized via K48 linkages
K63UbAb
an antibody to K63-linked Ubiquitin
a detection method used in a ubiq assay
KA
kinase activity
KAcAb
an antibody that detects acetylated lysines
a detection method used in an acetylation assay
KAcAb-ppt
an immunoprecipitation with an antibody that detects acetylated lysines
a detection method used in an acetylation assay
KD
kinase dead
KO
knockout
knockin
the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome
LB
lysis buffer
LexA
a tag derived from a bacterial repressor protein which activates transcription from a Lex operator-driven reporter gene when fused to activated transcription factors
a handle used to enable activated transcription factors to interact with a LexA-reporter
Ligand
anything that binds to a receptor on the outside surface of a cell
note: things that bind to nuclear receptors (eg estrogen binding to ERa) are classified as Ligands in this model.
LM
Listeria monocytogenes
Lmp1
Epstsein-Barr virus latent membrane protein-1
Lps
lipopolysaccaride from E.coli
Lps-Sa: from S.aureaus
Lps-S.min:  from Salmonella minnesota Re595
LSFC
Laser Scanning Fluorescence Cytometer
Luc
Luciferase
a detection method used in a Gal4-reporter assay
a detection method used in a LexA-reporter assay
a detection method used in a promo-reporter assay
a detection method used in a RE-reporter assay
m7GTP
7-methyl-GTP Sepharose, a synthetic analog of the mRNA 7-methylguanosine cap complex
a handle used to represent capped-mRNA
MalBP
Maltose binding protein
a handle used to describe or isolate a protein fused to MalBP
MamTwoHybrid
Mammalian Two Hybrid method
a detection method used in a boundby assay
Mant-GDP
3'-O-(N- methylanthraniloyl)guanosine 5'-diphosphate, a fluorescent analog of GDP
a detection method used in a GDP-dissociation assay
a detection method used in an IVGefA assay
Mant-GTP
3'-O-(N- methylanthraniloyl)guanosine 5'-triphosphate, a fluorescent analog of GTP
a detection method used in a GTP-association assay
MDP
muramyldipeptid
a microbial product, a component of petidoglycan
MicroArray:
a DNA microarray
a detection method used in a mRNA assay
mnr
mutation not revealed
modification:
a chemical modification of a protein after its translation
a Sort used in curation shorthand to describe the modification of a protein
mono
a modification used to describe protein monomers
MS
Mass Spectroscopy
a handle used when a protein is identified by Mass Spectroscopy
MS2
bacteriophage MS2 coat protein
a handle used to describe a protein fused to MS2
Mtb
Mycobacterium tuverculosis
mutation
a change in the sequence of a protein
a Sort used in curation shorthand to describe the mutation of a protein
MW
molecular weight
a handle used when a protein is identified by its migration on an SDS-PAGE gel
myr
myristoylation
a mutation that targets proteins to the cell membrane
note: when myr is used as a mutation it means that a myristolyation site (usually from Src) is fused at the N-terminus of an expressed protein
NativeWB
Native Western Blot
a detection method used in a dimerization assay
NEreporter
an method used to detect nuclear export
a detection method used in a nuc-export assay
NES
nuclear export signal
no-bkg-control
a warning added to an extra to indicate that inhibition of a positive change may be due to inhibition of the basal state rather than the change in state
Northern
Northern Blot
a detection method used in a mRNA assay
NS1
Nonstructured-Protein-1 from Influenza Virus
NucFree
a modification used to with GTP-binding proteins that have been depleted of GTP and GDP
oligo
an oligonucleotide
a modification used to represent oligomerization
on
a modification used to with genes that are actively expressing mRNA
p
a prefix used to designate a purified protein
In PL, a purified protein is an endogenous protein purified by biochemical techniques from cells or tissues
P100
P100 Fraction: a fraction containing cell membranes minus nuclei
a fraction used in a infraction assay
phos
a modification used to represent phosphorylation
phosAb
an antibody that detects a specific phosphorylation site when it is phosphorylated
a detection method used in an IVKA assay
a detection method used in a phos assay
a handle used to describe a protein identified by an antibody to a specific phosphorylation site
phosAb-ppt
an immunoprecitiptate by anti-phosphorylation site antibody
a detection method used in a phos assay
phosed
phosphorylated
Pi-release
release of inorganic phosphate into solvent
a detection method for a GTP-hydrolysis assay
PLL
Poly L-Lysine
PM1
plasma membrane fraction (method #1)
a fraction used in a infraction assay
PM2
plasma membrane fraction (method #2)
a fraction used in a infraction assay
poly
a modification used to represent polymerization
in some cases poly is followed by a number
these are used to distinguish between different Ubiquitin polymers accorded to the Ubiquitin ligases used
PPM
phosphopeptide mapping
prefix
a symbol used in curation shorthand to describe the origin of a protein
if the Protein has no prefix, then it is an endogenous protein
if prefixed with "x" then it is a protein expressed ectopically in a eukaryotic cell
if prefixed with "k" then it is a mutated protein expressed from a "knockin" sequence driven by the endogenous promoter.
if prefixed with "r" then it is a protein expressed in a prokaryotic cell and purified
if prefixed with "p" then it is a protein that has been purified from mammalian tissues
Protein
a molecule made of amino-acids
a family of BProteins
a composite of BProteins
pSAb
an antibody that detects phosphoserine
a detection method used in a Sphos assay
pSAb-ppt
an immunoprecipitate by anti-phosphoserine antibody
a detection method used in a Sphos assay
pSTAb
an antibody that detects phosphoserine/threonine
a detection method used in a STphos assay
pSTAb-ppt
an immunoprecipitate by anti-phosposerine/threonine antibody
a detection method used in a STphos assay
pTAb
an antibody that detects phosphoserine/threonine
a detection method used in a Tphos Assay
pTAb-ppt
an immunoprecipitate by anti-phospothreonine antibody
a detection method used in a Tphos Assay
pYAb
an antibody that detects phosphotyrosine
a detection method used in an IVKA assay
a detection method used in a Yphos assay
pYAb-ppt
an immunoprecipitate by anti-phosphotyrosine antibody
a detection method used in a Yphos assay
r
a prefix used to designate a protein expressed in bacteria or by In Vitro Translation
RE
response element
a handle used when a protein is identified by the DNA sequence it binds to
reqs
requires
rescue
re-expression of a protein in a knock-out cell
Resin
any solid support bound to a recombinant protein
a handle used when a recombinant protein is used as a Hook in a boundby assay
repressed by
used when a positive change is significantly increased in the absence of an endogenous protein
RIA
RadioImmunoAssay
a detection method used in a secretion assay
RNAi
interferring RNA
RPA
RNA Protection Assay
a detection method used in a mRNA assay
RTPCR
reverse transcriptase PCR
a detection method used in a mRNA assay
S100
S100 Fraction: a fraction containing soluble cytoplasmic proteins
a fraction used in a infraction assay
SABRE
Selective amplification via biotin- and restriction-mediated enrichment
SAP
Secreted Alkaline Phosphatase
a detection method used in a RE-reporter assay
Sepharose
a preparation of agarose used as a solid support for recombinant proteins
a handle used when a recombinant protein is used as a Hook in a boundby assay
sitenr
site not revealed
used when an antibody to a specific site on a protein is used as a detection method but the source does not report which site
snr
substrate not revealed
used in activity assays (IVKA, IVLKA, IVGefA) when the source does not report the substrate used
Sort
a Maude expression that specifies the type or classification of a term
SPR
Surface Plasmon Resonance
a detection method used in a boundby assay
SuAb
an antibody to Sumo
a detection method used in a sumo assay
SuAb-ppt
something immunoprecipitated with anti-Sumo antibody
a detection method used in a sumo assay
Subject
The first item in the first line of a datum - the focus of an experiment
In this model, the subject can be a Protein, a Family, a Composite, or a Gene.
Surface-strip
the removal of bound ligand on the surface of a cell
a detection method used in an internalization assay
synergistically
an adverb used with extras to describe an effect two treatments which is greater than sum of the effect of each treatment alone.
tAb
an antibody to a fusion tag on an expressed or recombinant Protein
TAD
Transactivation domain
Test-tube experiment
an experiment performed without cells or animals
TLC
Thin Layer Chromatography
a detection method used in a GTP-hydrolysis assay
a detection method used in a GTP-percent assay
a detection method used in an IVLKA assay
tnr
time not revealed
used when the time of a Stimulus is not reported
Treatment
the addition of something to cells or proteins to produce an observable change in state
tSuAb
an antibody to a tag on expressed Sumo
a detection method used in a sumo assay
tSuAb-ppt
something immunoprecipitated with an antibody to a tag on expressed Sumo
a detection method used in a sumo assay
tUbAb
an antibody to a tag on expressed Ubiquitin
a detection method used in a ubiq assay
tUbAb-ppt
something immunoprecipitated with an antibody to a tag on expressed Ubiquitin
a detection method used in a ubiq assay
UbAb
an antibody to Ubiquitin
a detection method used in a ubiq assay
UbAb-ppt
something immunoprecipitated with anti-Ubiquitin antibody
a detection method used in a ubiq assay
VP16
a herpes simplex virus (HSV)-encoded transcriptional activator protein
a handle used when an expressed protein is used as a Hook in a boundby assay using the MamTwoHybrid detection method.
WB
Western Blot
a detection method used in a boundby assay
a detection method used in a copptby assay
a detection method used in an infraction assay
a detection method used in a polymerization assay
a detection method used in a prot-exp assay
a detection method used in a secretion assay
a detection method used in a snaggedby assay
WBMS
Western Blot Mobility Shift
a detection method used in a cleavage assay
a detection method used in a phos assay
a detection method used in a sumo assay
a detection method used in a ubiq assay
a detection method used in a upshift assay
WBMS/PPase
Western Blot Mobility Shift before and after PPase treatment
a detection method used in a phos assay
WT
wild-type
any protein without a mutation or modification is wild-type
in some cases proteins are given the designation WT to distinguish it from the mutated or modified version.
x
a prefix used to designate a expressed protein expressed in eukaryotic cells
XFP
a fluorescent protein fused to an expressed protein
a handle used to identify a protein fused to a fluorescent protein
Xlink
chemical crosslinking that creates covalent bonds between proteins in close proximity
a detection method used in a boundby assay
a detection method used in a copptby assay
2D-PPMap
2-Dimensional PhosphoPeptide Mapping
a detection method used in a phos assay
2Tagppt
a method used to determine the oligomerization state of a protein
a detection method used in an oligomerization assay
3H
Hydrogen-3 (Tritium)
3H-acetate
acetate labelled with 3H
a detection method used in an acetylation assay
3H-acetate/CHX
treatment of cells with 3H-acetate in the presence of cyclohexamade (CHX)
a detection method used in an acetylation assay
3H-GDP:
Guanosine diphosphate labeled with 3H
a detection method used in a GDP-dissociation assay
a detection method used in an IVGefA assay
14C
Carbon-14
a handle used when 14C is used as a radiolabel
14C-acetyl-CoA
acetyl-CoA labeled with 14C
a detection method used in an acetylation assay
32P
Phosphorus-32
a handle used when 32P is used as a radiolabel
32P-ATP
Adenosine triphosphate labeled with 32P
a detection method used in a IVKA assay
a detection method used in a phos assay
32P-GTP
Guanosine triphosphate labeled with 32P.
a detection method used in a GTP-association assay
32Pi
metabolic labeling with 32P
a detection method used in a phos assay
32Pi-PAA
Phosphoamino acid analysis on proteins labeled metabolically with 32P
a detection method used in a Sphos assay
a detection method used in a STphos assay
a detection method used in a Tphos Assay
a detection method used in a Yphos assay
32P-release
release of 32P into solvent
a detection method for a GTP-hydrolysis assay
35S
Sulfur-35
a detection method used in a prot-exp assay
a handle used when 35S is used as a radiolabel
35S-GTPgS
Guanosine 5'-O-[gamma-thio]triphosphate, a nonhydrolyzable G-protein-activating analog of guanosine triphosphate (GTP), labeled with 35S.
a detection method used in a GTP-association assay
35S-pulse-chase
a method for determining protein stability
a detection method used in a prot-stability assay
125I
Iodine-125
a handle used when 125I is used as a radiolabel
125I-ligand
A ligand labelled with 125I
a detection method used in a surface-exp assay
125I-Tgfb1-XL
a handle used to identify TgfbR1 and/or TgfbR2