Network Web Service Clients
Name
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Description |
REST
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SOAP
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run JSON
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run JSP
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Java |
Perl |
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ClientNetWorkgetTFGene |
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 TFsin the gene-to-gene network where the interaction is a loop,but an arrow in the TF to gene graph. Note that autoregulationis 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. |
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ClientNetWorkgetTFOperon |
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 simplificationis 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. |
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ClientNetWorkgetTFGeneInOutDegree |
Get the transcription regulatory interactions for affecting a specific Transcription Factor (in-degree and out-degree). Notice that a regulon identifier is required. |
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ClientNetWorkgetTFTF |
Get the network between Transcription Factors (TFs). This is a subset of the TF-gene network, which contains only those interactions affecting the TFs expression. |
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ClientNetWorkgetSigmaTU |
Get the network between sigma factors and their corresponding transcribed Transcription Units. |
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ClientNetWorkgetSigmaGene |
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. |
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ClientNetWorkgetTFTU |
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. |
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Gene Web Service Client
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Name
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Description |
run JSP |
Download |
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Java |
Perl |
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| .class | .java | ||||
ClientGenegetGene |
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 |
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Operon Web Service Client
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Name
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Description |
run JSP
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Download
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Java |
Perl |
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| .class | .java | ||||
ClientOperongetOperon |
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 |
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Promoter Web Service Client
Name
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Description |
run JSP
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Download
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Java |
Perl |
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| .class | .java | ||||
ClientPromotergetPromoter |
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. |
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Regulon Web Service Client
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Name
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Description |
run JSP
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Download
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Java |
Perl |
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| .class | .java | ||||
ClientRegulongetRegulon |
Get the information contained in the regulon web page of RegulonDB. Notice that regulon identifier is different in each release, because it is regenerating. |
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TranscriptionUnit Web Service Client
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Name
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Description |
run JSP
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Download
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Java |
Perl |
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| .class | .java | ||||
ClientTranscriptionUnitgetgetTranscriptionUnit |
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 |
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DataUtilities Web Service Client
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Name
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Description |
run JSP
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Download
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Java
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Perl
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| .class | .java | ||||
ClientDataUtilitiesgetAllDNAObjectsInterval |
Get all DNA objects in a given interval. |
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Tool Web Service Client
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Name
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Description
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run JSP
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Download
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Java
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Perl
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| .class | .java | ||||
ClientToolgetDrawingTracesTool |
Get the image of all DNA objects in a given interval, obtained by the DrawingTracesTool. |
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DataSets Web Service Client
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Name
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Description |
run JSP
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Download
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Java
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Perl |
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| .class | .java | ||||
ClientDataSetsgetTFBindingSites |
Get all DNA sites recognized by Transcription Factors. |
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