Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0087

two component transcriptional regulator, LuxR (NCBI)

CircVis
Functional Annotations (7)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0087
(Mouseover regulator name to see its description)

RSP_0087 is regulated by 19 influences and regulates 26 modules.
Regulators for RSP_0087 (19)
Regulator Module Operator
RSP_0087 70 tf
RSP_0386 70 tf
RSP_1191 70 tf
RSP_1866 70 tf
RSP_2681 70 tf
RSP_3238 70 tf
RSP_0087 81 tf
RSP_0316 81 tf
RSP_0958 81 tf
RSP_1139 81 tf
RSP_1243 81 tf
RSP_1550 81 tf
RSP_1606 81 tf
RSP_1663 81 tf
RSP_1866 81 tf
RSP_1890 81 tf
RSP_2610 81 tf
RSP_3238 81 tf
RSP_3606 81 tf

Warning: RSP_0087 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
7860 2.20e-03 agAAttct.TT
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7861 3.70e-01 TTtTcatgttttc.g
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7882 9.70e-01 cAtg.Gc.gaacacagCgGgc
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7883 2.30e+01 taAcAgGaaAc
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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_0087

RSP_0087 is enriched for 7 functions in 3 categories.
Module neighborhood information for RSP_0087

RSP_0087 has total of 46 gene neighbors in modules 70, 81
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0087 RSP_0087 two component transcriptional regulator, LuxR (NCBI) 70, 81
RSP_0161 RSP_0161 Spermidine/putrescine-binding periplasmic protein (NCBI) 70, 102
RSP_0179 RSP_0179 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components TauA (NCBI) 70, 204
RSP_0345 RSP_0345 Possible ABC transporter, periplasmic binding protein (NCBI) 70, 204
RSP_0346 RSP_0346 ABC transporter, substrate binding protein (NCBI) 70, 204
RSP_0453 RSP_0453 hypothetical protein (NCBI) 52, 81
RSP_0683 RSP_0683 hypothetical protein (NCBI) 81, 127
RSP_0717 RSP_0717 hypothetical protein (NCBI) 48, 81
RSP_0798 RSP_0798 Neutral zinc metallopeptidases (NCBI) 52, 81
RSP_1070 RSP_1070 hypothetical protein (NCBI) 81, 162
RSP_1261 blrB blue-light receptor of the BLUF-family (NCBI) 81, 162
RSP_1356 RSP_1356 hypothetical protein (NCBI) 81, 92
RSP_1385 RSP_1385 hypothetical protein (NCBI) 81, 127
RSP_1397 RSP_1397 Glutathione S-transferase (NCBI) 52, 81
RSP_1413 RSP_1413 TRAP-T family transporter, periplasmic binding component (NCBI) 70, 102
RSP_1493 RSP_1493 Amidase (NCBI) 81, 278
RSP_1663 RSP_1663 putative transcriptional regulator, LacI family (NCBI) 81, 126
RSP_1665 RSP_1665 putative RhtB family transporter (NCBI) 81, 85
RSP_1666 LytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 81, 85
RSP_1747 bztA ABC glutamate/glutamine/aspartate/asparagine transporter, periplasmic substrate-binding protein (NCBI) 70, 102
RSP_1748 bztB ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztB (NCBI) 70, 204
RSP_1749 bztC ABC glutamate/glutamine/aspartate/asparagine transporter, inner membrane subunit BztC (NCBI) 70, 204
RSP_1750 bztD ABC glutamate/glutamine/aspartate/asparagine transporter, ATPase subunit bztD (NCBI) 70, 204
RSP_1812 RSP_1812 hypothetical protein (NCBI) 81, 221
RSP_1882 RSP_1882 ABC polyamine/opine transporter, ATPase subunit (NCBI) 70, 204
RSP_1883 RSP_1883 ABC polyamine/opine transporter, periplasmic substrate-binding protein (NCBI) 70, 204
RSP_1884 RSP_1884 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 70, 204
RSP_1886 RSP_1886 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 70, 204
RSP_2179 proV ABC glycine betaine/L-proline tranporter, ATPase subunit, ProV (NCBI) 70, 204
RSP_2180 proW ABC glycine betaine/L-proline transporter, inner membrane subunit (NCBI) 70, 204
RSP_2181 proX ABC glycine betaine/L-proline transporter, periplasmic substrate-binding subunit (NCBI) 52, 70
RSP_2211 RSP_2211 ABC transporter, periplasmic substrate-binding protein (NCBI) 67, 70
RSP_2320 RSP_2320 TRAP-T family transporter, periplasmic binding protein (NCBI) 16, 70
RSP_2397 RSP_2397 ABC putrescine transporter, periplasmic substrate-binding subunit (NCBI) 70, 291
RSP_2401 RSP_2401 putative 6-aminohexanoate-cyclic-dimer hydrolase (NCBI) 81, 127
RSP_2610 RSP_2610 trancriptional regulator, MerR family (NCBI) 81, 127
RSP_2611 ihfA Histone-like DNA-binding protein (IHF) (NCBI) 81, 127
RSP_2695 RSP_2695 Possible peptidoglycan binding protein (NCBI) 81, 207
RSP_2846 RSP_2846 putative 3-hydroxyisobutyrate dehydrogenase (NCBI) 81, 207
RSP_2886 glgC ADP-glucose pyrophosphorylase (NCBI) 16, 81
RSP_2923 RSP_2923 ABC branched amino acid transporter family, periplasmic substrate-binding protein (NCBI) 70, 195
RSP_2954 RSP_2954 hypothetical protein (NCBI) 81, 162
RSP_2955 RSP_2955 hypothetical protein (NCBI) 81, 162
RSP_3069 RSP_3069 NADPH-dependent FMN reductase (NCBI) 81, 207
RSP_3589 ihfB Integration host factor beta-subunit (NCBI) 48, 81
RSP_3730 RSP_3730 putative glutathione S-transferase (NCBI) 81, 207
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_0087
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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