Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0186

Transcriptional regulator, TetR family (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0186
(Mouseover regulator name to see its description)

RSP_0186 is regulated by 21 influences and regulates 8 modules.
Regulators for RSP_0186 (21)
Regulator Module Operator
RSP_0185 370 tf
RSP_0186 370 tf
RSP_0511 370 tf
RSP_0607 370 tf
RSP_1014 370 tf
RSP_1077 370 tf
RSP_2494 370 tf
RSP_3203 370 tf
RSP_3464 370 tf
RSP_3616 370 tf
RSP_3700 370 tf
RSP_0090 92 tf
RSP_0316 92 tf
RSP_0386 92 tf
RSP_0547 92 tf
RSP_0623 92 tf
RSP_0999 92 tf
RSP_1790 92 tf
RSP_1866 92 tf
RSP_3238 92 tf
RSP_3686 92 tf

Warning: RSP_0186 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
7904 9.10e-01 T.tcgAGa.AtttaT
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7905 6.20e-02 GgcgCgCttccacCTGcCcg
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8436 3.10e+01 gtaatagagCgcctcGaac.t
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8437 1.20e+02 ATttCgtTcT
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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_0186

RSP_0186 is enriched for 5 functions in 3 categories.
Module neighborhood information for RSP_0186

RSP_0186 has total of 45 gene neighbors in modules 92, 370
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0184 RSP_0184 putative N-carbamyl-L-amino acid amidohydrolase (NCBI) 92, 102
RSP_0185 RSP_0185 Transcriptional regulator, TetR family (NCBI) 92, 102
RSP_0186 RSP_0186 Transcriptional regulator, TetR family (NCBI) 92, 370
RSP_0204 RSP_0204 metallo-beta-lactamase family protein (NCBI) 285, 370
RSP_0605 RSP_0605 hypothetical protein (NCBI) 249, 370
RSP_0643 RSP_0643 periplasmic sensor signal transduction histidine kinase (NCBI) 92, 118
RSP_0787 RSP_0787 hypothetical protein (NCBI) 41, 92
RSP_0788 RSP_0788 hypothetical protein (NCBI) 41, 92
RSP_0872 def1 Formylmethionine deformylase (NCBI) 92, 195
RSP_0940 RSP_0940 ABC transporter, periplasmic substrate binding protein (NCBI) 92, 195
RSP_0941 RSP_0941 ABC transporter, ATPase subunit (NCBI) 92, 176
RSP_0942 RSP_0942 ABC transporter, inner membrane subunit (NCBI) 92, 176
RSP_0952 RSP_0952 Transglutaminase-like protein (NCBI) 249, 370
RSP_1308 RSP_1308 hypothetical protein (NCBI) 92, 102
RSP_1355 RSP_1355 Glycosyl transferase, family 51 (NCBI) 92, 102
RSP_1356 RSP_1356 hypothetical protein (NCBI) 81, 92
RSP_1567 RSP_1567 Probable sensory transduction histidine kinase (NCBI) 92, 195
RSP_1611 RSP_1611 sensor histidine kinase (NCBI) 35, 370
RSP_1612 RSP_1612 Sigma-54 dependent transcriptional regulator (NCBI) 370, 379
RSP_2006 amsA hypothetical protein (NCBI) 92, 329
RSP_2291 RSP_2291 hypothetical protein (NCBI) 14, 370
RSP_2429 RSP_2429 Glutathione-regulated potassium-efflux system protein, kefB (NCBI) 36, 370
RSP_2432 RSP_2432 hypothetical protein (NCBI) 31, 370
RSP_2433 cheY2 Chemotaxis response regulator, CheY2 (NCBI) 285, 370
RSP_2434 cheR1 Putative MCP methyltransferase, CheR1 (NCBI) 31, 370
RSP_2435 cheW1 Putative chemotaxis scaffold protein, CheW1 (NCBI) 31, 370
RSP_2436 cheA1 Chemotaxis histidine protein kinase, CheA1 (NCBI) 31, 370
RSP_2437 cheY1 chemotaxis response regulator, CheY1 (NCBI) 31, 370
RSP_2438 cheX Putative CheX protein (NCBI) 31, 370
RSP_2439 cheD putative chemotaxis protein, CheD (NCBI) 31, 370
RSP_2440 mcpA Methyl accepting chemotaxis protein (NCBI) 31, 370
RSP_2721 RSP_2721 hypothetical protein (NCBI) 38, 370
RSP_2830 RSP_2830 hypothetical protein (NCBI) 92, 139
RSP_2831 cobO Probable cob(I)alamin adenosyltransferase (NCBI) 92, 163
RSP_3018 RSP_3018 putative acyl-CoA dehydrogenase (NCBI) 304, 370
RSP_3060 cysE possible O-acetylserine synthase (NCBI) 141, 370
RSP_3062 fabG 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI) 141, 370
RSP_3116 RSP_3116 Conserved hypothetical membrane/transport protein (NCBI) 246, 370
RSP_3326 RSP_3326 Low molecular weight phosphotyrosine protein phosphatase (NCBI) 36, 92
RSP_3342 bfr Bacterioferritin (NCBI) 92, 118
RSP_3451 RSP_3451 TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI) 61, 370
RSP_3493 RSP_3493 hypothetical protein (NCBI) 220, 370
RSP_3495 RSP_3495 hypothetical protein (NCBI) 116, 370
RSP_3496 RSP_3496 Zinc carboxypeptidase A metalloprotease (M14) (NCBI) 220, 370
RSP_3498 RSP_3498 Antifreeze protein, type I (NCBI) 103, 370
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_0186
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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