Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0927 lyrS

transcriptional regulator, LyrR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0927
(Mouseover regulator name to see its description)

RSP_0927 is regulated by 12 influences and regulates 27 modules.
Regulators for RSP_0927 lyrS (12)
Regulator Module Operator
RSP_0071 276 tf
RSP_0087 276 tf
RSP_0927 276 tf
RSP_2853 276 tf
RSP_3324 276 tf
RSP_0071 60 tf
RSP_0927 60 tf
RSP_1274 60 tf
RSP_1590 60 tf
RSP_2853 60 tf
RSP_2922 60 tf
RSP_3324 60 tf

Warning: RSP_0927 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7840 8.40e+02 CGaaATc.TgaCcag
Loader icon
7841 2.80e+03 CATaCTTA
Loader icon
8266 1.90e+02 cAAaaAtcCcTgaC
Loader icon
8267 1.50e+03 CatGATtt
Loader icon
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_0927

RSP_0927 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_0927

RSP_0927 has total of 29 gene neighbors in modules 60, 276
Gene neighbors (29)
Gene Common Name Description Module membership
RSP_0030 RSP_0030 PAS sensor diguanylatecyclase/phosphodiesterase (NCBI) 60, 245
RSP_0041 RSP_0041 hypothetical protein (NCBI) 60, 245
RSP_0085 RSP_0085 multisensor hybrid histidine kinase (NCBI) 60, 259
RSP_0086 RSP_0086 hypothetical protein (NCBI) 60, 259
RSP_0399 RSP_0399 hypothetical protein (NCBI) 60, 276
RSP_0400 RSP_0400 hypothetical protein (NCBI) 60, 276
RSP_0401 RSP_0401 hypothetical protein (NCBI) 60, 276
RSP_0513 RSP_0513 hypothetical protein (NCBI) 60, 245
RSP_0861 RSP_0861 putative transmembrane hypothetical protein (NCBI) 60, 245
RSP_0927 lyrS transcriptional regulator, LyrR family (NCBI) 60, 276
RSP_1902 RSP_1902 Conserved hypothetical protein with TPR repeat (NCBI) 60, 276
RSP_1903 RSP_1903 Putative Flp pilus assembly protein TadC (NCBI) 60, 276
RSP_1904 RSP_1904 Putative Flp pilus assembly protein TadB (NCBI) 60, 276
RSP_1905 RSP_1905 Putative Flp pilus assembly protein ATPase CpaF (NCBI) 60, 276
RSP_1907 RSP_1907 Putative Flp pilus assembly protein ATPase CpaE (NCBI) 60, 276
RSP_1910 RSP_1910 Putative Flp pilus assembly protein CpaB (NCBI) 60, 276
RSP_3217 RSP_3217 Cache sensor protein (NCBI) 22, 60
RSP_3432 RSP_3432 methyl-accepting chemotaxis protein (NCBI) 60, 211
RSP_3708 mcpJ methyl accepting chemotaxis protein (NCBI) 60, 211
RSP_3725 RSP_3725 hypothetical protein (NCBI) 60, 276
RSP_3727 RSP_3727 hypothetical protein (NCBI) 60, 276
RSP_3768 RSP_3768 hypothetical protein (NCBI) 60, 276
RSP_6066 RSP_6066 hypothetical protein (NCBI) 270, 276
RSP_6127 RSP_6127 hypothetical protein (NCBI) 257, 276
RSP_6134 RSP_6134 hypothetical protein (NCBI) 165, 276
RSP_6187 RSP_6187 hypothetical protein (NCBI) 275, 276
RSP_6201 RSP_6201 hypothetical protein (NCBI) 56, 276
RSP_6220 RSP_6220 hypothetical protein (NCBI) 276, 277
RSP_6233 RSP_6233 gas vesicle operon protein (NCBI) 165, 276
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_0927
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend