EVIDENCE CLASSIFICATION
EcoCyc/RegulonDB team
We wish to classify the evidences associated to RegulonDB/EcoCyc objects as strong or weak.
This classification will be translated to the graphical display of objects, as weak evidence
objects will be plotted with dotted lines in contrast with strong evidences. If the same object
has different evidence sources, it should be displayed according to the strongest.
EXAMPLES OF GRAPHICAL DISPLAY
CAPTION:
RI = regulatory interaction
TU = transcription unit
FIG1. Promoter and TU with weak evidence
FIG2. Promoter, RI and TU with strong evidence
FIG3. TU with a weak evidence CRP RI and a strong DgsA RI. The evidence associated with
the promoter is strong, while the TU evidence is weak.
CLASSIFICATION
1. PROMOTERS
STRONG EVIDENCE
1.1 Transcription initiation mapping
Example: Primer extension, S1 mapping
1.2 RNA polymerase footprinting
1.3 Inferred from mutant phenotype
Example: Deletions of promoter regions
WEAK EVIDENCE
1.4 Automated inference of promoter position
Example: computational prediction
1.5 Human inference of promoter position
Example: possible promoter identified by expert by reading the sequence
1.6 Inferred by curator
1.7 Non-traceable author statement
Example: an article refers to a promoter citing a paper that cannot be traced
1.8 Traceable author statement
Example: an article refers to a promoter citing a traceable paper for which the curation
team has no access
1.9 Traceable author statement to experimental support
Example: an article refers to a promoter citing a paper that we have access to
2. REGULATORY_INTERACTIONS
STRONG EVIDENCE
2.1 Binding of cellular extracts
Example: Gel shift analysis
2.2 Binding of purified proteins
Example: Footprinting
2.3 Inferred from genetic interaction
Example: in vitro titration assay
2.4 Assay of purified protein
Example: in vitro transcription
2.5 Site mutation
Example: expression analysis when putative regulator binding sites are mutated
WEAK EVIDENCE
2.6 Gene expression analysis
Example: transcriptional fusions (lacZ)
2.7 Inferred from mutant phenotype
Example: a mutation on a transcription factors has a visible cell phenotype, and it is
inferred that the regulator might be regulating the genes responsible for the
phenotype
2.8 Automated inference based on similarity to consensus sequences
Example: computational method (ie PATSER) used to identify binding site
2.9 Human inference based on similarity to consensus sequences
Example: putative binding site identified by an expert by reading the sequence
2.10 Non-traceable author statement
2.11 Traceable author statement
2.12 Traceable author statement to experimental support
3. TRANSCRIPTION UNITS
STRONG EVIDENCE
3.1 Length of transcript experimentally determined
Example: Northern blot
3.2 Polar mutation
Example: a mutation on the promoter or the first gene affects the expression of
neighbouring genes
3.3 Boundaries of transcription experimentally identified
Example: when promoter and terminator are identified
3.4 Automated inference that a single-gene directon is a transcription unit
Example: a gene surrounded by genes in opposite transcription directions
WEAK EVIDENCE
3.5 Inferred through co-regulation
Example: 2+ adjacent genes show the same expression pattern across conditions
3.6 Inferred by a human based on computational evidence
3.7 Products of adjacent genes in the same biological process
3.8 Inferred computationally without human oversight
Example: computational results with no expert review
3.9 Inferred by curator
3.10 Non-traceable author statement
3.11 Traceable author statement
3.12 Traceable author statement to experimental support
TAXONOMY
UNIQUE-ID - |EV-IC|
UNIQUE-ID - |EV-IC-ADJ-GENES-SAME-BIO-PROCESS
UNIQUE-ID - |EV-EXP|
UNIQUE-ID - |EV-EXP-IMP|
UNIQUE-ID - |EV-EXP-IMP-SITE-MUTATION|
UNIQUE-ID - |EV-EXP-IMP-REACTION-BLOCKED|
UNIQUE-ID - |EV-EXP-IMP-POLAR-MUTATION|
UNIQUE-ID - |EV-EXP-IMP-REACTION-ENHANCED|
UNIQUE-ID - |EV-EXP-IGI|
UNIQUE-ID - |EV-EXP-IGI-FUNC-COMPLEMENTATION|
UNIQUE-ID - |EV-EXP-IEP|
UNIQUE-ID - |EV-EXP-IEP-COREGULATION|
UNIQUE-ID - |EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS|
UNIQUE-ID - |EV-EXP-IDA|
UNIQUE-ID - |EV-EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS|
UNIQUE-ID - |EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS|
UNIQUE-ID - |EV-EXP-IDA-PART-PURIFIED-PROTEIN|
UNIQUE-ID - |EV-EXP-IDA-PURIFIED-PROTEIN|
UNIQUE-ID - |EV-EXP-IDA-PURIFIED-PROTEIN-MULTSPECIES|
UNIQUE-ID - |EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION|
UNIQUE-ID - |EV-EXP-IDA-TRANSCRIPTION-INIT-MAPPING|
UNIQUE-ID - |EV-EXP-IDA-UNPURIFIED-PROTEIN|
UNIQUE-ID - |EV-EXP-IDA-BOUNDARIES-DEFINED|
UNIQUE-ID - |EV-EXP-IDA-RNA-POLYMERASE-FOOTPRINTING|
UNIQUE-ID - |EV-EXP-TAS|
UNIQUE-ID - |EV-EXP-IPI|
UNIQUE-ID - |EV-COMP|
UNIQUE-ID - |EV-COMP-AINF|
UNIQUE-ID - |EV-COMP-AINF-FN-FROM-SEQ|
UNIQUE-ID - |EV-COMP-AINF-SIMILAR-TO-CONSENSUS|
UNIQUE-ID - |EV-COMP-AINF-SINGLE-DIRECTON|
UNIQUE-ID - |EV-COMP-AINF-POSITIONAL-IDENTIFICATION|
UNIQUE-ID - |EV-COMP-HINF|
UNIQUE-ID - |EV-COMP-HINF-FN-FROM-SEQ|
UNIQUE-ID - |EV-COMP-HINF-POSITIONAL-IDENTIFICATION|
UNIQUE-ID - |EV-COMP-HINF-SIMILAR-TO-CONSENSUS|
UNIQUE-ID - |EV-AS|
UNIQUE-ID - |EV-AS-TAS|
UNIQUE-ID - |EV-AS-NAS|
DESCRIPCION
//
UNIQUE-ID - |EV-IC|
COMMON-NAME - Inferred by curator
COMMENT - Inferred by curator. An assertion was inferred by a curator from relevant
information such as other assertions in a database.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP|
COMMON-NAME - Inferred from experiment
COMMENT - Inferred from experiment. The evidence for an assertion comes from a
wet-lab experiment of some type.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IMP-SITE-MUTATION|
COMMON-NAME - Site mutation
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT - A cis-mutation in the DNA sequence of the transcription-factor binding site
interferes with the operation of the regulatory function. This is considered strong evidence for the
existence and functional role of the DNA binding site.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IMP-REACTION-BLOCKED|
COMMON-NAME - Reaction blocked in mutant
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Mutant is characterized, and blocking of reaction is demonstrated.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IMP-POLAR-MUTATION|
COMMON-NAME - Polar mutation
PERTAINS-TO - |Transcription-Units|
COMMENT - If a mutation in a gene or promoter prevents expression of the downstream genes
due to a polar effect, the mutated gene is clearly part of the transcription unit.
COMMENT-INTERNAL It is used for TUs with two or more genes. It may be wrong to assign a TU on such evidence if
the first gene is a regulator which regulates a promoter upstream of the second gene.
//
UNIQUE-ID - |EV-EXP-IMP-REACTION-ENHANCED|
COMMON-NAME - Reaction enhanced in mutant
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Gene is isolated and over-expressed, and increased accumulation of reaction
product is observed.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IGI-FUNC-COMPLEMENTATION|
COMMON-NAME - Inferred by functional complementation
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Protein activity inferred by isolating its gene and performing functional
complementation of a well characterized heterologous mutant for the protein.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IEP-COREGULATION|
COMMON-NAME - Inferred through co-regulation
PERTAINS-TO - |Transcription-Units|
COMMENT - Inferred through co-regulation. A transcription unit is inferred because a set of
adjacent genes that are transcribed in the same direction exhibit similar
expression patterns under a range of environmental conditions.
COMMENT-INTERNAL –
Comentario adicional:
A TU is defined assuming there is ony one promoter upsream of all genes of the TU. However,
although unlikely, there may be a promoter for each gene and all of them co-regulated and
active and inactive under the same conditions.
//
UNIQUE-ID - |EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS|
COMMON-NAME - Gene expression analysis
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT - The expression of the gene is analyzed through a transcriptional fusion (i.e. lacZ),
and a difference in expression levels is observed when the regulatory protein is present (wild
type) vs in its absence. Note that this evidence does not eliminate the possiblity of an indirect
effect of the regulator on the regulated gene.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS|
COMMON-NAME - Binding of cellular extracts
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT - There exists physical evidence of the binding of cellular extracts containing
a regulatory protein to its DNA binding site. This can be either by
footprinting or mobility shift assays.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS|
COMMON-NAME - Binding of purified proteins
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-PART-PURIFIED-PROTEIN|
COMMON-NAME - Assay of partially purified protein
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Protein partially purified from specific species (or from
heterologous expression vector), and activity measured through in vitro
assay.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-PURIFIED-PROTEIN|
COMMON-NAME - Assay of purified protein
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Protein purified to homogeneity from specific species (or from heterologous
expression vector), and activity measured through in vitro assay.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-PURIFIED-PROTEIN-MULTSPECIES|
COMMON-NAME - Assay of protein purified from mixed culture
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Protein purified from mixed culture or other multispecies environment (such as,
infected plant or animal tissue), and activity measured through in vitro assay.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION|
COMMON-NAME - Length of transcript experimentally determined
PERTAINS-TO - |Transcription-Units|
COMMENT - The length of the (transcribed) RNA is experimentally determined. The length of the
mRNA is compared with that of the DNA sequence and by this means the number of genes
transcribed are established.
COMMENT-INTERNAL Comentario adicional: This is strong evidence, very hard to refute.
//
UNIQUE-ID - |EV-EXP-IDA-TRANSCRIPTION-INIT-MAPPING|
COMMON-NAME - Transcription initiation mapping
PERTAINS-TO - |Promoters|
COMMENT - The transcription start site is identified by primer extension.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-UNPURIFIED-PROTEIN|
COMMON-NAME - Assay of unpurified protein
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Direct assay of unpurified protein. Presence of a protein activity is indicated by an
assay.
However, the precise identity of the protein with that activity is not established by
this experiment (protein has not been purified).
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA-BOUNDARIES-DEFINED|
COMMON-NAME - Boundaries of transcription experimentally identified
PERTAINS-TO - |Transcription-Units|
COMMENT - Sites or genes bounding the transcription unit are experimentally identified. Several
possible cases exist, such as defining the boundaries of a transcription unit with an
experimentally identified promoter and terminator, or with a promoter and a downstream gene
that is transcribed in the opposite direction, or with a terminator and an upstream gene that is
transcribed in the opposite direction.
COMMENT-INTERNAL Comentario adicional:
There could be a terminator or promoter not yet identified within the TU.
//
UNIQUE-ID - |EV-EXP-IDA-RNA-POLYMERASE-FOOTPRINTING|
COMMON-NAME - RNA polymerase footprinting
PERTAINS-TO - |Promoters|
COMMENT - The binding of RNA polymerase to a DNA region (the promoter) is shown by
footprinting.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IMP|
COMMON-NAME - Inferred from mutant phenotype
COMMENT - IMP inferred from mutant phenotype.
The assertion was inferred from a mutant phenotype such as
o Any gene mutation/knockout
o Overexpression/ectopic expression of wild-type or mutant genes
o Anti-sense experiments
o RNA interference experiments
o Specific protein inhibitors
o Complementation
Comment: Inferences made from examining mutations or
abnormal levels of only the product(s) of the gene of interest are covered by code EV-IMP
(compare to code EV-IGI). Use this code for experiments that use antibodies
or other specific inhibitors of RNA or protein activity, even though no
gene may be mutated (the rationale is that EV-IMP is used where an
abnormal situation prevails in a cell or organism).
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IGI|
COMMON-NAME - Inferred from genetic interaction
COMMENT - IGI inferred from genetic interaction.
The assertion was inferred from a genetic interaction such as
o \,Traditional\, genetic interactions such as suppressors, synthetic
lethals, etc.
o Functional complementation
o Inference about one gene drawn from the phenotype of a mutation
in a different gene
This category includes any combination of alterations in the sequence
(mutation) or expression of more than one gene/gene product. This
category can therefore cover any of the IMP experiments that are done
in a non-wild-type background, although we prefer to use it only when
all mutations are documented. When redundant copies of a gene must all
be mutated to see an informative phenotype, use the IGI code. (Yes,
this implies some organisms, such as mouse, will have far, far more IGI
than IMP annotations.)
IMP also covers phenotypic similarity: a phenotype that is informative
because it is similar to that of another independent phenotype (which
may have been described earlier or documented more fully) is IMP (not IGI).
We have also decided to use this category for situations where a
mutation in one gene (gene A) provides information about the function,
process, or component of another gene (gene B; i.e. annotate gene B
using IGI).
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-TAS|
COMMON-NAME - Traceable author statement to experimental support
COMMENT - Traceable author statement to experimental support. The assertion was made in a
publication -- such as a review or
in another database -- that itself did not describe an experiment supporting the
assertion. However, the statement did reference another publication describing an experiment
that supports the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IPI|
COMMON-NAME - Inferred from physical interaction
COMMENT - IPI inferred from physical interaction
The assertion was inferred from a physical interaction such as
o 2-hybrid interactions
o Co-purification
o Co-immunoprecipitation
o Ion/protein binding experiments
This code covers physical interactions between the gene product of
interest and another molecule (or ion, or complex). For functions such
as protein binding or nucleic acid binding, a binding assay is
simultaneously IPI and IDA; IDA is preferred because the assay
directly detects the binding. For both IPI and IGI, it would be good
practice to qualify them with the gene/protein/ion.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IEP|
COMMON-NAME - Inferred from expression pattern
COMMENT - IEP inferred from expression pattern.
The assertion was inferred from a pattern of expression data such as
o Transcript levels (e.g. Northerns, microarray data)
o Protein levels (e.g. Western blots)
COMMENT-INTERNAL //
UNIQUE-ID - |EV-EXP-IDA|
COMMON-NAME - Inferred from direct assay
COMMENT - IDA inferred from direct assay.
The assertion was inferred from a direct experimental assay such as
o Enzyme assays
o In vitro reconstitution (e.g. transcription)
o Immunofluorescence
o Cell fractionation
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP|
COMMON-NAME - Inferred by computational analysis
COMMENT - Inferred from computation. The evidence for an assertion comes from a
computational analysis. The assertion itself might have been made
by a person or by a computer, that is, EV-COMP does not specify whether
manual interpretation of the computation occurred.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-AINF-FN-FROM-SEQ|
COMMON-NAME - Automated inference of function from sequence
PERTAINS-TO - RNA
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - Artificial inference of function from sequence. A computer inferred a gene function
based on sequence,
profile, or structural similarity (as computed from sequence) to one or more other sequences.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-AINF-SIMILAR-TO-CONSENSUS|
COMMON-NAME - Automated inference based on similarity to consensus sequences
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT - A DNA sequence similar to previously known consensus sequences is
computationally identified.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-AINF-SINGLE-DIRECTON|
COMMON-NAME - Automated inference that a single-gene directon is a transcription unit
PERTAINS-TO - |Transcription-Units|
COMMENT - Artificial inference of transcription unit based on single-gene directon. Existence of
a single-gene transcription unit
for gene G is inferred computationally by the existence of upstream and downstream genes
transcribed in the
opposite direction of G.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-AINF-POSITIONAL-IDENTIFICATION|
COMMON-NAME - Automated inference of promoter position
PERTAINS-TO - |Promoters|
COMMENT - Automated inference of promoter position relative to the -10 and -35 boxes.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-HINF-FN-FROM-SEQ|
COMMON-NAME - Human inference of function from sequence
PERTAINS-TO - RNA
PERTAINS-TO - |Proteins|
PERTAINS-TO - |Enzymatic-Reactions|
COMMENT - A person inferred, or reviewed a computer inference of, gene function based
on sequence, profile, or structural similarity (as computed from sequence) to
one or more other sequences.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-HINF-POSITIONAL-IDENTIFICATION|
COMMON-NAME - Human inference of promoter position
PERTAINS-TO - |Promoters|
COMMENT - A person inferred, or reviewed a computer inference of, promoter position relative to
the -10 and -35 boxes.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-HINF-SIMILAR-TO-CONSENSUS|
COMMON-NAME - Human inference based on similarity to consensus sequences
PERTAINS-TO - |DNA-Binding-Sites|
COMMENT - A person inferred, or reviewed a computer inference of, sequence
function based on similarity to a consensus sequence.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-AINF|
COMMON-NAME - Inferred computationally without human oversight
COMMENT - Artificial inference. A computer inferred this assertion through one of many possible
methods such as
sequence similarity, recognized motifs or consensus sequence, etc. When a person made the
inference
from computational evidence, use EV-HINF
COMMENT-INTERNAL //
UNIQUE-ID - |EV-COMP-HINF|
COMMON-NAME - Inferred by a human based on computational evidence
COMMENT - Human inference. A curator or author inferred this assertion after review of one or
more possible types
of computational evidence such as sequence similarity, recognized motifs or consensus
sequence, etc.
When the inference was made by a computer in an automated fashion, use EV-AINF.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-AS|
COMMON-NAME - Author statement
COMMENT - Author statement. The evidence for an assertion comes from an author
statement in a publication, where that publication does not state direct experimental support
for the assertion. Ordinarily, this code will not be used directly -- generally one of
its child codes, EV-TAS or EV-NAS, will be used instead.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-AS-TAS|
COMMON-NAME - Traceable author statement
COMMENT - Traceable author statement. The assertion was made in a publication -- such as a
review or
in another database -- that itself did not describe an experiment supporting the
assertion. The statement referenced another publication that supported the assertion,
but it is unclear whether that publication described an experiment that supported
the assertion. The difference between the codes EV-EXP-TAS and EV-AS-TAS
is that the former code is used when it is certain that experimental evidence supports the
assertion, and the latter code is used when there is a possibility that an experiment was
not done to support the assertion.
In general, references to the primary literature are preferred,
but this code can be used when the original article is difficult to locate.
COMMENT-INTERNAL //
UNIQUE-ID - |EV-AS-NAS|
COMMON-NAME - Non-traceable author statement
COMMENT - Non-traceable author statement. The assertion was made in a publication such as
a review, a meeting abstract,
or another database without a reference to a publication describing an experiment that supports
the assertion.
COMMENT-INTERNAL //