RegulonDB 11.2: Evidence Classification

Evidence Classification in RegulonDB

Scientific knowledge advances incrementally. At any point, we base broad conclusions on assertions of varying degrees of confidence. RegulonDB classifies evidence supporting particular assertions essentially based on the methods used to generate them. We do so to make explicit the complex mixture of more or less well supported specific claims that support broader conclusions (Weiss et al., 2013) In RegulonDB version 11.1 we made several changes to the collection of evidence types. We made changes to the evidence codes to make them more informative and more precise since we indicate the corresponding method. We increased the number of high throughput evidence types. Finally, we updated the collection of combinations of independent methods that increase the confidence levels. The details can be found in the sections on additive evidence below.

We classify the evidence supporting knowledge as ’Weak’, ’Strong ’ or ’Confirmed ’.

Weak evidence: Single evidence with more ambiguous conclusions, where alternative explanations, indirect effects, or potential false positives are prevalent, as well as computational predictions; for instance gel mobility shift assays with cell extracts or gene expression analysis.

Strong evidence: Single evidence with direct physical interaction or solid genetic evidence with a low probability for alternative explanations; for instance, footprinting with purified protein or site mutation.

Confirmed: is assigned, if objects are supported by at least two independent types of strong evidence with mutually excluding false positives. This approach is based essentially on the methods used to validate results and exclude alternative explanations in scientific research.

Confidence is assigned in two stages:

In stage I: we classify single evidence into weak or strong.

In stage II: we define combinations of independent evidence in a process termed “additive evidence” (previously described as Cross-Validation in (Weiss et al., 2013), that enable multiple weak evidence types to support an object with a strong (S) confidence level, as well as multiple strong types to support the higher “confirmed (C)” level of an object.

Stage I. Classification of Individual Evidence Types

As mentioned before, in RegulonDB version 11.1 we made changes to the collection of evidence types; we changed the evidence codes so now they indicate the corresponding method ((for instance Transcription initiation mapping is now encoded as primer extension assay for transcription start site determination evidence or S1 nuclease protection assay evidence for transcription start site determination evidence ).

Description
Single evidence is classified into weak or strong evidence (see above), depending on the confidence level of the associated methodologies.

1. Promoters and transcription start sites (TSSs)
Promoters are defined in bacteria by the DNA region specifically bound by RNA polymerase to initiate transcription. A TSS is the precise first nucleotide that is transcribed, different methods identify promoters or TSSs. They are jointly classified here.		Evidence Code	Evidence Category	Evidence Group
Strong Evidence	1.1 RNA polymerase footprinting The binding of RNA polymerase to a DNA region (the promoter) is shown by footprinting.	EXP-IDA-RNA-POLYMERASE-FOOTPRINTING	Classical experiment	9
	1.2 RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates	RS-EPT-CBR	High-throughput protocol
	1.3 Site mutation 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.	EXP-IMP-SITE-MUTATION	Classical binding	1
	1.4 Transcription initiation mapping The transcription start site is identified by primer extension.	EXP-IDA-TRANSCRIPTION-INIT-MAPPING	Classical experiment	15
Weak Evidence	1.5 A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence. Human inference based on similarity to consensus sequences	COMP-HINF-SIMILAR-TO-CONSENSUS	non-experimental	7
	1.6 Author hypothesis Author hypothesis. The hypothesis is in a publication, but it was clearly indicated in the publication that there was no experimental evidence, or limited evidence, supporting the hypothesis. This code can be used, for example, for paper chemistry metabolic pathways, which are pathways drawn from the author's best estimation.	AS-HYPO	non-experimental
	1.7 Author statement 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.	AS	non-experimental
	1.8 Automated inference based on sequence pattern discovery A sequence found by pattern discovery using computational methods.	COMP-AINF-PATTERN-DISCOVERY	non-experimental	7
	1.9 Automated inference based on similarity to consensus sequences A DNA sequence similar to previously known consensus sequences is computationally identified.	COMP-AINF-SIMILAR-TO-CONSENSUS	non-experimental	7
	1.10 Automated inference of promoter position Automated inference of promoter position relative to the -10 and -35 boxes.	COMP-AINF-POSITIONAL-IDENTIFICATION	non-experimental	7
	1.11 High-throughput transcription initiation mapping The transcription start site is identified using a high-throughput experimental modified RACE approach.	EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP	High-throughput protocol	10
	1.12 Human inference of promoter position A person inferred, or reviewed a computer inference of, promoter position relative to the -10 and -35 boxes.	COMP-HINF-POSITIONAL-IDENTIFICATION	non-experimental	7
	1.13 Inferred by a human based on computational evidence 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.	COMP-HINF	non-experimental	7
	1.14 Inferred by computational analysis 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.	COMP	non-experimental	7
	1.15 Inferred by curator Inferred by curator. An assertion was inferred by a curator from relevant information such as other assertions in a database.	IC	non-experimental
	1.16 Inferred computationally without human oversight Automated 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-COMP-HINF.	COMP-AINF	non-experimental	7
	1.17 Inferred from direct assay IDA inferred from direct assay. The assertion was inferred from a direct experimental assay such as Enzyme assays In vitro reconstitution (e.g. transcription) Immunofluorescence Cell fractionation	EXP-IDA	Classical binding
	1.18 Inferred from experiment Inferred from experiment. The evidence for an assertion comes from a wet-lab experiment of some type.	EXP	nd
	1.19 Inferred from expression pattern IEP inferred from expression pattern. The assertion was inferred from a pattern of expression data such as Transcript levels (e.g. Northerns, microarray data) Protein levels (e.g. Western blots)	EXP-IEP	Classical expression	3
	1.20 Inferred from mutant phenotype IMP inferred from mutant phenotype. The assertion was inferred from a mutant phenotype such as Any gene mutation/knockout Overexpression/ectopic expression of wild-type or mutant genes Anti-sense experiments RNA interference experiments Specific protein inhibitors 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).	EXP-IMP	Classical binding
	1.21 Inferred from physical interaction IPI inferred from physical interaction The assertion was inferred from a physical interaction such as 2-hybrid interactions Co-purification Co-immunoprecipitation 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.	EXP-IPI	Classical experiment
	1.22 Non-traceable author statement 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.	AS-NAS	non-experimental
	1.23 Traceable author statement 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.	AS-TAS	non-experimental
	1.24 Traceable author statement to experimental support 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.	EXP-TAS	non-experimental
	1.25 high throughput RNA-seq evidence Transcriptome analysis by RNA-seq (high-throughput sequencing of fragmented cDNA molecules) provides evidence for regulatory binding sites, based on a comparative analysis of the expression of potential target genes.	EXP-IEP-RNA-SEQ	High-throughput expression	3

2. Regulatory interactions
A regulatory interaction is defined, depending on the type of evidence, as the transcription factor (TF)-regulated gene interaction (TF-gene), or more specifically as the TF-DNA binding site interaction.		Evidence Code	Evidence Category	Evidence Group
Strong Evidence	2.1 Binding of purified proteins	EXP-IDA-BINDING-OF-PURIFIED-PROTEINS	Classical binding	2
Strong Evidence	2.2 Site mutation 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.	EXP-IMP-SITE-MUTATION	Classical binding	1
Weak Evidence	2.3 A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence. Human inference based on similarity to consensus sequences	COMP-HINF-SIMILAR-TO-CONSENSUS	non-experimental	7
	2.4 Assay of protein purified to homogeneity Direct assay of purified protein. Protein purified to homogeneity, and activity measured using an in vitro assay. Expression host is unspecified.	EXP-IDA-PURIFIED-PROTEIN	Classical binding
	2.5 Author statement 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.	AS	non-experimental
	2.6 Automated inference based on sequence pattern discovery A sequence found by pattern discovery using computational methods.	COMP-AINF-PATTERN-DISCOVERY	non-experimental	7
	2.7 Automated inference based on similarity to consensus sequences A DNA sequence similar to previously known consensus sequences is computationally identified.	COMP-AINF-SIMILAR-TO-CONSENSUS	non-experimental	7
	2.8 Binding of cellular extracts 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.	EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS	Classical binding	6
	2.9 ChIP-PCR evidence used in manual assertion A type of chromatin immunoprecipation-PCR evidence that is used in a manual assertion.	EXP-CHIP-PCR-MANUAL	High-throughput binding	4
	2.10 ChIP-chip evidence used in manual assertion A type of chromatin immunoprecipation-chip evidence that is used in a manual assertion.	EXP-CHIP-CHIP-MANUAL	High-throughput binding	4
	2.11 ChIP-exo evidence used in manual assertion A type of chromatin immunoprecipation-exonuclease evidence that is used in a manual assertion.	EXP-CHIP-EXO-MANUAL	High-throughput binding	4
	2.12 ChIP-seq evidence used in manual assertion A type of chromatin immunoprecipation-seq evidence that is used in a manual assertion.	EXP-CHIP-SEQ-MANUAL	High-throughput binding	4
	2.13 Gene expression analysis 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.	EXP-IEP-GENE-EXPRESSION-ANALYSIS	Classical expression	3
	2.14 Inferred by a human based on computational evidence 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.	COMP-HINF	non-experimental	7
	2.15 Inferred by computational analysis 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.	COMP	non-experimental	7
	2.16 Inferred by curator Inferred by curator. An assertion was inferred by a curator from relevant information such as other assertions in a database.	IC	non-experimental
	2.17 Inferred computationally without human oversight Automated 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-COMP-HINF.	COMP-AINF	non-experimental	7
	2.18 Inferred from Biological aspect from Ancestor A type of phylogenetic evidence whereby an aspect of a descendent is inferred through the characterization of an aspect of a ancestral gene.	COMP-IBA	non-experimental
	2.19 Inferred from direct assay IDA inferred from direct assay. The assertion was inferred from a direct experimental assay such as Enzyme assays In vitro reconstitution (e.g. transcription) Immunofluorescence Cell fractionation	EXP-IDA	Classical binding
	2.20 Inferred from expression pattern IEP inferred from expression pattern. The assertion was inferred from a pattern of expression data such as Transcript levels (e.g. Northerns, microarray data) Protein levels (e.g. Western blots)	EXP-IEP	Classical expression	3
	2.21 Inferred from genetic interaction IGI inferred from genetic interaction. The assertion was inferred from a genetic interaction such as Traditional genetic interactions such as suppressors, synthetic lethals, etc. Functional complementation 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).	EXP-IGI	Classical binding
	2.22 Inferred from mutant phenotype IMP inferred from mutant phenotype. The assertion was inferred from a mutant phenotype such as Any gene mutation/knockout Overexpression/ectopic expression of wild-type or mutant genes Anti-sense experiments RNA interference experiments Specific protein inhibitors 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).	EXP-IMP	Classical binding
	2.23 Manually curated inference based on sequence pattern discovery A sequence found by pattern discovery using computational methods and reviewed by a person.	COMP-HINF-PATTERN-DISCOVERY	non-experimental	7
	2.24 Non-traceable author statement 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.	AS-NAS	non-experimental
	2.25 Reaction blocked in mutant Mutant is characterized, and blocking of reaction is demonstrated.	EXP-IMP-REACTION-BLOCKED	Classical binding
	2.26 Traceable author statement 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.	AS-TAS	non-experimental
	2.27 Traceable author statement to experimental support 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.	EXP-TAS	non-experimental
	2.28 high throughput ChIP-chip evidence A type of chromatin immunoprecipation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.	EXP-CHIP-CHIP	High-throughput binding	4
	2.29 high throughput ChIP-exo evidence A type of chromatin immunoprecipation evidence that uses gamma-exonuclease to digest transcription-factor-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.	EXP-CHIP-EXO	High-throughput binding	4
	2.30 high throughput ChIP-seq evidence A type of chromatin immunoprecipation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.	EXP-CHIP-SEQ	High-throughput binding	4
	2.31 high throughput DNA Affinity Purification (DAP) Sequencing An in vitro TF-DNA binding assay that allows rapid generation of genome-wide binding site maps for a large number of TFs, while capturing genomic DNA properties that impact binding in vivo.	EXP-DAP-SEQ	High-throughput binding
	2.32 high throughput Genomic SELEX-chip evidence Technique to identify DNA binding sites for a transcription factor based on genomic systematic evolution of ligands by exponential enrichment (SELEX), variant of the classic SELEX protocol.	EXP-GSELEX	High-throughput binding	5
	2.33 high throughput RNA-seq evidence Transcriptome analysis by RNA-seq (high-throughput sequencing of fragmented cDNA molecules) provides evidence for regulatory binding sites, based on a comparative analysis of the expression of potential target genes.	EXP-IEP-RNA-SEQ	High-throughput expression	3
	2.34 high throughput expression microarray evidence Transcriptome analysis by expression microarrays provide evidence for regulatory binding sites, based on a comparative analysis of the expression of potential target genes.	EXP-IEP-MICROARRAY	High-throughput expression	3

3. Transcription factor functional conformation
Most dedicated TFs have usually two conformations, one with a non-covalent bound allosteric metabolite, or a covalent phosphorylation (holo conformation), and one as a free protein or multimer (the apo conformation). There are exceptions to this statement. We call functional conformation the one that is capable of binding to its specific binding sites and perform its activation or repression activity. For the sake of functional conformation evidence the experiments below have to be considered with and without effector.		Evidence Code	Evidence Category	Evidence Group
Strong Evidence	3.1 Assay of protein purified to homogeneity from a heterologous host Direct assay of protein purified from a heterologous host. Recombinant protein purified to homogeneity from a heterologous host expressing cloned gene(s), and activity measured using an in vitro assay.	EXP-IDA-PURIFIED-PROTEIN-HH	Classical experiment
	3.2 Assay of protein purified to homogeneity from its native host Direct assay of protein purified from its native host. Protein purified to homogeneity from its native host, and activity measured using an in vitro assay.	IDA-PURIFIED-PROTEIN-NH	Classical experiment
	3.3 Binding of purified proteins	EXP-IDA-BINDING-OF-PURIFIED-PROTEINS	Classical binding	2
	3.4 Inferred by functional complementation Protein activity inferred by isolating its gene and performing functional complementation of a well characterized heterologous mutant for the protein.	EXP-IGI-FUNC-COMPLEMENTATION	Classical experiment
	3.5 Site mutation 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.	EXP-IMP-SITE-MUTATION	Classical binding	1
Weak Evidence	3.6 Assay of partially-purified protein Direct assay of partially purified protein from a specific organism. Protein partially purified, and activity measured using an in vitro assay. Expression host is unspecified.	EXP-IDA-PART-PURIFIED-PROTEIN	Classical experiment
	3.7 Assay of protein partially-purified from a heterologous host Direct assay of protein partially purified from a heterologous host. Recombinant protein partially purified from a heterologous host expressing cloned gene(s), and activity measured using an in vitro assay.	EXP-IDA-PART-PURIFIED-PROTEIN-HH	Classical experiment
	3.8 Assay of protein partially-purified from its native host Direct assay of protein partially purified from its native host. Protein partially purified from its native host, and activity measured using an in vitro assay.	EXP-IDA-PART-PURIFIED-PROTEIN-NH	Classical experiment
	3.9 Assay of protein purified to homogeneity Direct assay of purified protein. Protein purified to homogeneity, and activity measured using an in vitro assay. Expression host is unspecified.	EXP-IDA-PURIFIED-PROTEIN	Classical binding
	3.10 Assay of unpurified protein Direct assay of unpurified protein. Presence of a protein activity is indicated by an assay, but the protein has not been purified. Expression host is unspecified.	EXP-IDA-UNPURIFIED-PROTEIN	Classical experiment
	3.11 Assay of unpurified protein expressed in its native host Direct assay of unpurified protein from its native host. Presence of a protein activity is indicated by an assay performed with an organism, but the precise identity of the protein responsible for that activity is not established, since the protein has not been purified.	EXP-IDA-UNPURIFIED-PROTEIN-NH	Classical experiment
	3.12 Automated inference of function by sequence orthology A computer inferred a function based on the function of an orthologous protein in another organism.	COMP-AINF-SEQ-ORTHOLOGY	non-experimental
	3.13 Automated inference of function from sequence Automated 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.	COMP-AINF-FN-FROM-SEQ	non-experimental
	3.14 Binding of cellular extracts 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.	EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS	Classical binding	6
	3.15 Gene expression analysis 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.	EXP-IEP-GENE-EXPRESSION-ANALYSIS	Classical expression	3
	3.16 Human inference of function based on ortholog with experimental function in closely related strain or species.	COMP-HINF-ORTHOLOGY-EXP	non-experimental
	3.17 Human inference of function from sequence 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.	COMP-HINF-FN-FROM-SEQ	non-experimental
	3.18 Inferred by a human based on computational evidence 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.	COMP-HINF	non-experimental	7
	3.19 Inferred by computational analysis 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.	COMP	non-experimental	7
	3.20 Inferred computationally without human oversight Automated 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-COMP-HINF.	COMP-AINF	non-experimental	7
	3.21 Inferred from Sequence Alignment Human inference based on a sequence alignment. Sequence similarity with experimentally characterized gene products, as determined by alignments, either pairwise or multiple (tools such as BLAST, ClustalW, MUSCLE).	COMP-HINF-ISA	non-experimental
	3.22 Inferred from Sequence Model Human inference based on evidence from some kind of statistical model of a sequence or group of sequences, which is used to make a prediction about the function of a protein or RNA. - Prediction methods for non-coding RNA genes such as tRNASCAN-SE, Snoscan, and Rfam - Predicted presence of recognized functional domains or membership in protein families, as determined by tools such as profile Hidden Markov Models (HMMs), including Pfam and TIGRFAM - Predicted protein features using tools such as TMHMM (transmembrane regions), SignalP (signal peptides on secreted proteins), and TargetP (subcellular localization) - any other kind of domain modeling tool or collections of them such as SMART, PROSITE, PANTHER, InterPro, etc. - An entry in the with field of a GO annotation is required when the model used is an object with an accession number (as found with Pfam, TIGRFAM, InterPro, PROSITE, Rfam, etc.) The with field may be left blank for tools such as tRNAscan and Snoscan where there is not an object with an accession to point to.	COMP-HINF-ISM	non-experimental
	3.23 Inferred from direct assay IDA inferred from direct assay. The assertion was inferred from a direct experimental assay such as Enzyme assays In vitro reconstitution (e.g. transcription) Immunofluorescence Cell fractionation	EXP-IDA	Classical binding
	3.24 Inferred from experiment Inferred from experiment. The evidence for an assertion comes from a wet-lab experiment of some type.	EXP	nd
	3.25 Inferred from expression pattern IEP inferred from expression pattern. The assertion was inferred from a pattern of expression data such as Transcript levels (e.g. Northerns, microarray data) Protein levels (e.g. Western blots)	EXP-IEP	Classical expression	3
	3.26 Inferred from genetic interaction IGI inferred from genetic interaction. The assertion was inferred from a genetic interaction such as Traditional genetic interactions such as suppressors, synthetic lethals, etc. Functional complementation 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).	EXP-IGI	Classical binding
	3.27 Inferred from mutant phenotype IMP inferred from mutant phenotype. The assertion was inferred from a mutant phenotype such as Any gene mutation/knockout Overexpression/ectopic expression of wild-type or mutant genes Anti-sense experiments RNA interference experiments Specific protein inhibitors 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).	EXP-IMP	Classical binding
	3.28 Inferred from physical interaction IPI inferred from physical interaction The assertion was inferred from a physical interaction such as 2-hybrid interactions Co-purification Co-immunoprecipitation 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.	EXP-IPI	Classical experiment

4. Transcription units
		Evidence Code	Evidence Category	Evidence Group
Strong Evidence	4.1 Length of transcript experimentally determined 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.	EXP-IDA-TRANSCRIPT-LEN-DETERMINATION	Classical experiment	11
Strong Evidence	4.2 Polar mutation 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.	EXP-IMP-POLAR-MUTATION	Classical experiment	12
Weak Evidence	4.3 Author hypothesis Author hypothesis. The hypothesis is in a publication, but it was clearly indicated in the publication that there was no experimental evidence, or limited evidence, supporting the hypothesis. This code can be used, for example, for paper chemistry metabolic pathways, which are pathways drawn from the author's best estimation.	AS-HYPO	non-experimental
	4.4 Automated inference that a single-gene directon is a transcription unit Automated 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.	COMP-AINF-SINGLE-DIRECTON	non-experimental	13
	4.5 Boundaries of transcription experimentally identified 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.	EXP-IDA-BOUNDARIES-DEFINED	Classical experiment	14
	4.6 Inferred by a human based on computational evidence 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.	COMP-HINF	non-experimental	7
	4.7 Inferred by curator Inferred by curator. An assertion was inferred by a curator from relevant information such as other assertions in a database.	IC	non-experimental
	4.8 Inferred computationally without human oversight Automated 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-COMP-HINF.	COMP-AINF	non-experimental	7
	4.9 Inferred from Biological aspect from Ancestor A type of phylogenetic evidence whereby an aspect of a descendent is inferred through the characterization of an aspect of a ancestral gene.	COMP-IBA	non-experimental
	4.10 Inferred from direct assay IDA inferred from direct assay. The assertion was inferred from a direct experimental assay such as Enzyme assays In vitro reconstitution (e.g. transcription) Immunofluorescence Cell fractionation	EXP-IDA	Classical binding
	4.11 Inferred from expression pattern IEP inferred from expression pattern. The assertion was inferred from a pattern of expression data such as Transcript levels (e.g. Northerns, microarray data) Protein levels (e.g. Western blots)	EXP-IEP	Classical expression	3
	4.12 Inferred from mutant phenotype IMP inferred from mutant phenotype. The assertion was inferred from a mutant phenotype such as Any gene mutation/knockout Overexpression/ectopic expression of wild-type or mutant genes Anti-sense experiments RNA interference experiments Specific protein inhibitors 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).	EXP-IMP	Classical binding
	4.13 Inferred through co-regulation 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.	EXP-IEP-COREGULATION	Classical experiment
	4.14 No biological data available EV-ND is intended for use in GO annotations. Use of the EV-ND evidence code indicates that the annotator at the contributing database found no information that allowed making an annotation to any term indicating specific knowledge from the ontology in question (molecular function, biological process, or cellular component) as of the date indicated. This code should be used only for annotations to the root terms, molecular function ; GO:0003674, biological process ; GO:0008150, or cellular component ; GO:0005575, which, when used in annotations, indicate that no knowledge is available about a gene product in that aspect of GO.	ND	non-experimental
	4.15 Non-traceable author statement 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.	AS-NAS	non-experimental
	4.16 Products of adjacent genes in the same biological process A transcription unit is inferred because there is a set of adjacent genes, encoded in the same direction, coding for products that participate in the same metabolic pathway or biological process. Sometimes, these genes code for subunits of the same protein.	IC-ADJ-GENES-SAME-BIO-PROCESS	non-experimental
	4.17 Traceable author statement 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.	AS-TAS	non-experimental
	4.18 Traceable author statement to experimental support 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.	EXP-TAS	non-experimental

Stage II. Assignment of confidence level based on additive evidence types

Following the same logic described in (Weiss et al., 2013) we integrate multiple evidence by combining independent types of evidence, with the intention to confirm individual objects and mutually exclude false positives. It follows the same principles of science as applied by wet-lab scientists, where data are confirmed by repetitions on the one hand, and by additional experimental strategies to exclude alternative explanations on the other. This approach allows us to combine classic methods from molecular biology and genomic high throughput (HT) methods.

Additive evidence (called "cross-validation" in previous releases of RegulonDB) requires that the combined methods are independent, that is, do not share major sources of false positives or common raw materials. In this version the evidence codes were assigned to an evidence group, different evidence groups correspond to independent methods. Evidence codes from the same evidence group cannot be combined to upgrade the object confidence level. Some evidence groups are shared among diverse object types, i.e. EXP-IMP-SITE-MUTATION is associated with regulatory interactions and also with promoters, while other classes are exclusive of an object type.

Objects that are supported by multiple types of independent weak (W) evidence are classified as strong evidence (S). A third confidence score "confirmed"(C) is assigned to objects that are supported by two types of independent strong evidence. In the table below are indicated the combinations of evidence groups that result in upgrade to strong or confirmed confidence level of an object. i.e. the combination (8/10/7) results in a confirmed confidence level; it happens when the object has at least one evidence code from the evidence groups 8, 10 and 7.

The downloadable datasets contain all the individual evidence types so users can either construct their own combinations or use the three confidence levels (W,S,C).

1. Promoters and transcription start sites (TSSs)
Cross Validation (1/9)	1: (EXP-IMP-SITE-MUTATION) 9: (EXP-IDA-RNA-POLYMERASE-FOOTPRINTING)
Cross Validation (1/10/7)	1: (EXP-IMP-SITE-MUTATION) 10: (EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP) 7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-POSITIONAL-IDENTIFICATION \| COMP-HINF-POSITIONAL-IDENTIFICATION \| COMP-HINF \| COMP \| COMP-AINF)
Cross Validation (9/10/7)	9: (EXP-IDA-RNA-POLYMERASE-FOOTPRINTING) 10: (EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP) 7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-POSITIONAL-IDENTIFICATION \| COMP-HINF-POSITIONAL-IDENTIFICATION \| COMP-HINF \| COMP \| COMP-AINF)
Strong Evidence	Cross Validation (10/7)	10: (EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP) 7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-POSITIONAL-IDENTIFICATION \| COMP-HINF-POSITIONAL-IDENTIFICATION \| COMP-HINF \| COMP \| COMP-AINF)

2. Regulatory interactions
Confirmed Evidence	Cross Validation (1/2)	1: (EXP-IMP-SITE-MUTATION) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (4/5/3/1)	4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (7/4/3/1)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (7/5/3/1)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (6/4/3/1)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (6/5/3/1)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (7/6/3/1)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 1: (EXP-IMP-SITE-MUTATION)
	Cross Validation (4/5/3/2)	4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (7/4/3/2)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (7/5/3/2)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (6/4/3/2)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (6/5/3/2)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
	Cross Validation (7/6/3/2)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY) 2: (EXP-IDA-BINDING-OF-PURIFIED-PROTEINS)
Strong Evidence	Cross Validation (4/5/3)	4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)
	Cross Validation (7/4/3)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)
	Cross Validation (7/5/3)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)
	Cross Validation (6/4/3)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 4: (EXP-CHIP-PCR-MANUAL \| EXP-CHIP-CHIP-MANUAL \| EXP-CHIP-EXO-MANUAL \| EXP-CHIP-SEQ-MANUAL \| EXP-CHIP-CHIP \| EXP-CHIP-EXO \| EXP-CHIP-SEQ) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)
	Cross Validation (6/5/3)	6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 5: (EXP-GSELEX) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)
	Cross Validation (7/6/3)	7: (COMP-HINF-SIMILAR-TO-CONSENSUS \| COMP-AINF-PATTERN-DISCOVERY \| COMP-AINF-SIMILAR-TO-CONSENSUS \| COMP-HINF \| COMP \| COMP-AINF \| COMP-HINF-PATTERN-DISCOVERY) 6: (EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS) 3: (EXP-IEP-GENE-EXPRESSION-ANALYSIS \| EXP-IEP \| EXP-IEP-RNA-SEQ \| EXP-IEP-MICROARRAY)

3. Transcription units
Confirmed Evidence	Cross Validation (11/12)	11: (EXP-IDA-TRANSCRIPT-LEN-DETERMINATION) 12: (EXP-IMP-POLAR-MUTATION)
Strong Evidence	Cross Validation (13/14)	13: (COMP-AINF-SINGLE-DIRECTON) 14: (EXP-IDA-BOUNDARIES-DEFINED)

RegulonDB