Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0316

Transcriptional regulator, LuxR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
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_0316
(Mouseover regulator name to see its description)

RSP_0316 is regulated by 17 influences and regulates 21 modules.
Regulators for RSP_0316 (17)
Regulator Module Operator
RSP_0316 250 tf
RSP_0386 250 tf
RSP_0999 250 tf
RSP_1139 250 tf
RSP_1164 250 tf
RSP_1518 250 tf
RSP_1550 250 tf
RSP_1871 250 tf
RSP_2324 250 tf
RSP_0316 341 tf
RSP_0327 341 tf
RSP_0386 341 tf
RSP_0999 341 tf
RSP_1139 341 tf
RSP_1550 341 tf
RSP_1871 341 tf
RSP_2425 341 tf

Warning: RSP_0316 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
8218 1.80e-05 Ag.cgat.t..cg.ttt.ttgaag
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8219 6.00e-02 AagGatGAcggA
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8384 1.20e+01 GCaTCcttctCtGctcaTTGGCTa
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8385 1.70e+01 AtTccTtCAtC
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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_0316

RSP_0316 is enriched for 5 functions in 3 categories.
Module neighborhood information for RSP_0316

RSP_0316 has total of 42 gene neighbors in modules 250, 341
Gene neighbors (42)
Gene Common Name Description Module membership
RSP_0316 RSP_0316 Transcriptional regulator, LuxR family (NCBI) 250, 341
RSP_0380 RSP_0380 hypothetical protein (NCBI) 250, 341
RSP_0386 RSP_0386 Cold-shock DNA-binding domain protein (NCBI) 250, 341
RSP_0427 RSP_0427 hypothetical protein (NCBI) 250, 257
RSP_0548 RSP_0548 hypothetical protein (NCBI) 185, 250
RSP_0589 RSP_0589 hypothetical protein (NCBI) 185, 250
RSP_0754 RSP_0754 hypothetical protein (NCBI) 35, 250
RSP_0822 RSP_0822 hypothetical protein (NCBI) 35, 341
RSP_1001 RSP_1001 hypothetical protein (NCBI) 127, 341
RSP_1133 RSP_1133 hypothetical protein (NCBI) 56, 341
RSP_1138 RSP_1138 two component transcriptional regulator, winged helix family (NCBI) 64, 250
RSP_1139 RSP_1139 transcriptional regulator, MarR family (NCBI) 64, 250
RSP_1141 RSP_1141 hypothetical protein (NCBI) 35, 250
RSP_1518 prrA PrrA (RegA), Response regulator involved in oxygen regulation of photosynthesis genes (NCBI) 250, 341
RSP_1522 RSP_1522 hypothetical protein (NCBI) 162, 341
RSP_1550 RSP_1550 regulatory proteins, IclR family (NCBI) 127, 341
RSP_1551 RSP_1551 putative glyoxalase family protein (NCBI) 35, 250
RSP_1678 RSP_1678 putative RecO protein (NCBI) 35, 341
RSP_1681 RSP_1681 two-component transcriptional regulator, winged helix family (NCBI) 223, 341
RSP_1682 RSP_1682 Two-component sensor histidine kinase (NCBI) 223, 341
RSP_1683 RSP_1683 putative kinase/phosphatase (NCBI) 267, 341
RSP_1684 RSP_1684 P-loop ATPase (NCBI) 223, 341
RSP_1685 RSP_1685 PTS system, IIA component (NCBI) 223, 341
RSP_1686 RSP_1686 Putative Phosphocarrier HPr protein (NCBI) 87, 341
RSP_1794 RSP_1794 putative lytic transglycosylase (NCBI) 10, 250
RSP_1859 ppdK Pyruvate phosphate dikinase (NCBI) 248, 341
RSP_1871 RSP_1871 Transcriptional regulator, GntR family (NCBI) 162, 341
RSP_1917 RSP_1917 hypothetical protein (NCBI) 250, 289
RSP_1972 RSP_1972 hypothetical protein (NCBI) 250, 341
RSP_1973 RSP_1973 Probable SufE protein (NCBI) 250, 341
RSP_2175 RSP_2175 ABC transporter, ATPase subunit (NCBI) 48, 341
RSP_2554 RSP_2554 hypothetical protein (NCBI) 35, 250
RSP_2618 RSP_2618 Putative hemolysin (NCBI) 10, 341
RSP_2621 ctrA two component transcriptional regulator, winged helix family (NCBI) 250, 341
RSP_2631 RSP_2631 USG protein (NCBI) 35, 250
RSP_2729 RSP_2729 Probable Restriction endonuclease (NCBI) 195, 250
RSP_2762 RSP_2762 hypothetical protein (NCBI) 250, 341
RSP_2782 aqpZ aquaporin z, Major Intrinsic Protein (MIP) Family (NCBI) 250, 341
RSP_2847 RSP_2847 hypothetical protein (NCBI) 185, 250
RSP_2937 RSP_2937 hypothetical protein (NCBI) 35, 341
RSP_2940 RSP_2940 hypothetical protein (NCBI) 174, 341
RSP_3007 RSP_3007 hypothetical protein (NCBI) 48, 250
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_0316
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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