RegulonDB 11.2: Method Detail

RegulonDB

Method Detail Network

Name

getTFGene

Description

Get the network between Transcription Factors (TF) and their regulated genes.

The elements of this network are TFs and genes.The data enable users to describe the network as either, regulatory gene to affected gene, or TF to regulated gene.The graphs will be similar, except for autoregulation of TFs in the gene-to-gene network where the interaction is a loop,but an arrow in the TF to gene graph. Note that autoregulation is far from an exceptional case. The case of heterodimers is more complex, since there will be one node to the protein (i.e. IHF); but two nodes for each gene encoding a homodimer (i.e. himA and himB). Furthermore, a quite complex module occurs when the heterodimer complex is auto-regulated.

Synopsis

 public static java.lang.String getTFGene()

Input Parameters

                              none

Output Parameters

type: String
 Description:
TFName(regulator)
 GeneName(regulated)
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getTFOperon

Description

Get the network between Transcription Factors (TF) and their regulated operons.

In this network type, the number of interactions and nodes is even smaller than the TF-TUs (Transcription Units), since an operon may contain multiple TUs. The prize of this simplification is that an edge is not directly related to a single mechanism or regulated promoter. For instance, a single CRP site participates in both, the activation and repression of galp1 and galp2 promoters, respectively; in both cases, transcribing the galETK operon. This is represented as two interactions in the TF-TU network (two edges); while a single edge with a dual function represents the dual effect of CRP on the operon.

Synopsis

 public static java.lang.String getTFOperon()

Input Parameters

                              none

Output Parameters

type: String
 Description:
  TFName(regulator)
 OperonName(regulated)[operon genes]
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getTFGeneInOutDegree

Description

Get the transcription regulatory interactions for affecting a specific Transcription Factor (in-degree and out-degree). Notice that a regulon identifier is required.

Synopsis

 public static java.lang.String getTFGeneInOutDegree(java.lang.String TFName)

Input Parameters

                              TFName - TF's Name

Output Parameters

String
 Description:
TFName(regulator)
 GeneName(regulated)
 Sign(effect) 
 Evidence Code of the interaction
 separated by tab.

Name

getTFTF

Description

Get the network between Transcription Factors (TFs).

This is a subset of the TF-gene network, which contains only those interactions affecting the expression of TFs.

Synopsis

 public static java.lang.String getTFTF()

Input Parameters

                              none

Output Parameters

type: String
 Description:
TFName(regulator)
 TFName(regulated)
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getSigmaGene

Description

Get the network between sigma factors and their corresponding transcribed genes.

Notice that in this network, the interactions refer to transcription; however, a positive function is assigned for refer to the positive effect of sigma in the gene transcription.

Synopsis

 public static java.lang.String getSigmaGene()

Input Parameters

                              none

Output Parameters

String
 Description:
SigmaFactorName(regulator)
 GeneName(regulated)
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getSigmaTU

Description

Get the network between sigma factors and their corresponding transcribed Transcription Units.

Synopsis

 public static java.lang.String getSigmaTU()

Input Parameters

                              none

Output Parameters

type: String
 Description:
SigmaFactorName(regulator)
 TUName(regulated)[promoter name]
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getTFTU

Description

Get the network between TFs and their regulated transcription units (TUs).

Each outgoing edge describes relation of a TF with a transcription unit (group of genes transcribed from a single promoter).; making it a much smaller network than the TF-gene network. The interactions of this network are at a single promoter by definition.

Synopsis

 public static java.lang.String getTFTU()

Input Parameters

                              none

Output Parameters

type: String
 Description:
TFName(regulator)
 TUName(regulated)[promoter name]
 Sign(effect)
 Evidence Code of the interaction
 separated by tab.

Name

getColumnNames

Description

Get columns names

Synopsis

 public static java.lang.String getColumnNames(java.lang.String methodName)

Input Parameters

                              WSName

Output Parameters

type: String
 Description:
 The result contains the column names
 separated by tab.

Method Detail Gene

Name

getGene

Description

Get the information contained in the gene web page of RegulonDB.

Example:
http://regulondb.ccg.unam.mx/gene?organism=ECK12&term=ECK120000050&format=jsp&type=gene

Synopsis

 public static java.lang.String getGene(java.lang.String objectId)

Input Parameters

                              Name: objectId 
 type: String 
 Description:

Output Parameters

type: String
 Description:
 GENE
 Gene name:
 Synonyms:
 Map positions:
 Strand:
 Sequence:
 External database links
 DatabaseName : ID
 PRODUCT
 Product name:
 Synonyms:
 Sequence:
 Regulator Family:
 Molecular weight:
 Isoelectric Point:
 Motifs
 Type   Position        Sequence
 TypeValue  PositionValue  SequenceValue
 Classification:
 Notes:
 Evidence:
 EvicenceCode: Evidence Description
 References:
 External database links
 DatabaseName : ID
 OPERON
 Operon Name:
 Operon arrangement
 Transcription unit     Promoter name

Method Detail Operon

Name

getOperon

Description

Get the information contained in the operon web page of RegulonDB.

Example:
http://regulondb.ccg.unam.mx/operon?term=ECK120015033&format=jsp&organism=ECK12&type=operon

Synopsis

 public static java.lang.String getOperon(java.lang.String objectId)

Input Parameters

                              Name: objectId 
 type: String 
 Description:

Output Parameters

type: String
 Description:
 OPERON
 Operon Name:
 TRANSCRIPTION UNIT (TU)
 TU Name:
 Synonyms:
 Genes:
 Evidence:
 EvicenceCode: Evidence Description
 References:
 PROMOTER
 Promoter Name:
 Pos +1:
 Sigma Factor:
 Distance to the start of the first gene:
 Sequence:
 Evidence
 Reference
 TERMINATOR
 Type:
 Sequence:
 Evidence
 Reference
 REGULATION (BINDING SITES BS)
 Transcription Factor
 Function
 Promoter
 BS left position
 BS right position
 BS Central relative position
 BS sequence
 BS Evidence Code
 BS Reference

Method Detail Promoter

Name

getPromoter

Description

Get the information contained in the promoter section of operon web page in RegulonDB; also, the transcription unit(s) transcribed by the promoter are added.

Synopsis

 public static java.lang.String getPromoter(java.lang.String objectId)

Input Parameters

                              Name: objectId 
 type: String 
 Description:

Output Parameters

type: String
 Description:
 PROMOTER
 Promoter Name:
 Pos +1:
 Sigma Factor:
 Sequence:
 Evidence
 Reference
 Distance to the start of the first gene:
 Transcription Units
 Transcription Unit Name:
 Transcribed Genes:

Method Detail Regulon

Name

getRegulon

Description

Get the information contained in the regulon web page of RegulonDB.

Notice that regulon identifier is different in each release, because it is regenerating.

Synopsis

 public static java.lang.String getRegulon(java.lang.String objectId)

Input Parameters

                              Name: objectId 
 type: String 
 Description:

Output Parameters

type: String
 Description:
 TRANSCRIPTION FACTOR
 Transcription Factor Name:
 Connectivity class
 Sensing Class
 Synonyms
 Gene Name
 Functional conformation(s)
 Coregulators
 Notes
 REGULATION 
 Functional conformation(s)
 Function
 Regulated Promoter
 Regulated Genes
 BS left position
 BS right position
 BS Central relative position
 BS sequence
 BS Evidence Code
 BS Reference

Method Detail Trascription Unit

Name

getTranscriptionUnit

Description

Get the information contained in the Transcription Unit section of the operon web page in RegulonDB.

Example:
http://regulondb.ccg.unam.mx/operon?term=ECK120015033&format=jsp&organism=ECK12&type=operon

Synopsis

 public static java.lang.String getTranscriptionUnit(java.lang.String objectId)

Input Parameters

                              Name: objectId 
 type: String 
 Description:

Output Parameters

type: String
 Description:
 TRANSCRIPTION UNIT (TU)
 TU Name
 Synonyms
 Genes
 References
 PROMOTER
 Promoter Name
 Pos +1
 Sigma Factor
 Distance to the start of the first gene
 Sequence
 Evidence
 Reference
 TERMINATOR
 Type
 Sequence
 Evidence
 Reference
 REGULATION (BINDING SITES ÔøΩÔøΩÔøΩBS)
 Transcription Factor
 Function
 Promoter
 BS left position
 BS right position
 BS Central relative position
 BS sequence
 BS Evidence Code
 BS Reference

Method Detail DataUtilities

Name

getAllDNAObjectInterval

Description

Get all DNA objects in a given interval.

Synopsis

 public static java.lang.String getAllDNAObjectInterval(int absPosLeft, int absPosRight, java.lang.String strand, java.util.Vector typeObject, boolean covered)

Input Parameters

                              Name: absPosLeft 
 type: int 
 Description:

 Name: absPosRight 
 type: int 
 Description:

 Name: strand 
 type: String 
 Description:

 Name: typeObject 
 type: Vector 
 Description: 

 Name: covered 
 type: boolean 
 Description:

Output Parameters

type: String
 Description:
 ObjectType
LeftPosition
RightPosition
Strand
ObjectColor
LineWidth
LineType
LabelName
LabelFont
LabelColor
LabelSize
ToolTip
LineColor
ObjectId

Name

getAllDNAObjectInterval

Description

Get all DNA objects in a given interval.

Synopsis

 public static java.lang.String getAllDNAObjectInterval(int absPosLeft, int absPosRight, java.lang.String strand, java.lang.String typeObject, boolean covered)

Input Parameters

                              Name: absPosLeft 
 type: int 
 Description:

 Name: absPosRight 
 type: int 
 Description:

 Name: strand 
 type: String 
 Description:

 Name: typeObject 
 type: String 
 Description: 

 Name: covered 
 type: boolean 
 Description:

Output Parameters

type: String
 Description:
 ObjectType
LeftPosition
RightPosition
Strand
ObjectColor
LineWidth
LineType
LabelName
LabelFont
LabelColor
LabelSize
ToolTip
LineColor
ObjectId

Method Detail Tool

Name

getDrawingTracesTool

Description

Get the image of all DNA objects in a given interval, obtained by the DrawingTracesTool.

Synopsis

 public static java.lang.Object[] getDrawingTracesTool(java.lang.String file, java.lang.String[] parameters)

Input Parameters

                              Name: file 
 type: String 
 Description:

 Name: args 
 type: String[] 
 Description:

Output Parameters

type: Object []
 Description:
 Object[0] = String Log
 Object[1] = byte[] image
 Object[2] = String Html

Name

getDrawingTracesTool

Description

Get the image of all DNA objects in a given interval, obtained by the DrawingTracesTool.

Synopsis

 public static byte[] getDrawingTracesTool(java.lang.String file)

Input Parameters

                              Name: file 
 type: String 
 Description:

Output Parameters

type: byte[]
 Description:
 image

Method Detail DataSets

Name

getTFBindingSites

Description

Get all DNA sites recognized by a Transcription Factor.

Synopsis

 public static java.lang.String getTFBindingSites()

Input Parameters

                              none

Output Parameters

type: String
 Description:
 Transcription Factor (TF) identifier assigned by RegulonDB
 TF name
 TF binding site (TF-bs) identifier assigned by RegulonDB
 TF-bs left end position in the genome
 TF-bs right end position in the genome
 DNA strand where the  TF-bs is located
 TF-Gene interaction identifier assigned by RegulonDB (related to the TF gene interactions file)
 Transcription unit regulated by the TF
 Gene expression effect caused by the TF bound to the  TF-bs  (+ activation, - repression, +- dual, ? unknown)
 Central relative position of TF-bs, relative to Transcription Start Site
 TF-bs sequence (upper case)
 Evidence that supports the existence of the TF-bs
 separated by tab.

Name

getColumnNames

Description

Get Columns Names

Synopsis

 public static java.lang.String getColumnNames(java.lang.String methodName)

Input Parameters

                              WSName

Output Parameters

type: String
 Description:
 The result contains the column names
 separated by tab.

RegulonDB