Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3665

transcriptional regulator, LuxR family (NCBI)

CircVis
Functional Annotations (8)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3665
(Mouseover regulator name to see its description)

RSP_3665 is regulated by 20 influences and regulates 21 modules.
Regulators for RSP_3665 (20)
Regulator Module Operator
RSP_0386 214 tf
RSP_0443 214 tf
RSP_0623 214 tf
RSP_0760 214 tf
RSP_1518 214 tf
RSP_2324 214 tf
RSP_2346 214 tf
RSP_2494 214 tf
RSP_2572 214 tf
RSP_2963 214 tf
RSP_3616 214 tf
RSP_3665 214 tf
RSP_0722 384 tf
RSP_0728 384 tf
RSP_2171 384 tf
RSP_2236 384 tf
RSP_2533 384 tf
RSP_2840 384 tf
RSP_2922 384 tf
RSP_3665 384 tf
Regulated by RSP_3665 (21)
Module Residual Genes
3 0.50 26
5 0.43 25
17 0.50 25
33 0.58 19
59 0.41 25
130 0.48 28
142 0.45 19
175 0.55 32
178 0.60 11
185 0.50 26
214 0.50 25
216 0.49 29
221 0.54 24
237 0.56 16
311 0.52 25
335 0.55 9
343 0.57 9
344 0.46 17
374 0.49 25
375 0.58 9
384 0.55 23
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
8148 6.50e-12 cgAAc.tttCtTtcgcaacaaa.
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8149 8.40e-03 AAgTcacttga
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8458 2.40e+01 Tttctccga.GgctA
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8459 8.70e+03 tCg.TtcAAaggcctGctcttGc
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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_3665

RSP_3665 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
Module neighborhood information for RSP_3665

RSP_3665 has total of 47 gene neighbors in modules 214, 384
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0150 RSP_0150 chase sensor signal transducdtion histidine kinase (NCBI) 87, 214
RSP_0368 RSP_0368 CTP synthase (NCBI) 65, 384
RSP_0407 RSP_0407 putative lactate dehydrogenase (NCBI) 175, 384
RSP_0613 RSP_0613 hypothetical protein (NCBI) 214, 325
RSP_0713 RSP_0713 hypothetical protein (NCBI) 96, 384
RSP_0722 RSP_0722 transcriptional regulator, AsnC family (NCBI) 254, 384
RSP_0760 mucS transcriptional regulator, MarR family (NCBI) 17, 214
RSP_0894 RSP_0894 hypothetical protein (NCBI) 175, 384
RSP_1031 RSP_1031 Endonuclease III (NCBI) 110, 384
RSP_1041 RSP_1041 Malonyl CoA synthetase (NCBI) 214, 363
RSP_1099 LspA signal peptidase II (NCBI) 113, 384
RSP_1127 ElaA acetyltransferase, GNAT family (NCBI) 214, 231
RSP_1161 RSP_1161 3'-Phosphadenosine 5'-phosphosulfate 3'-phosphatase (NCBI) 109, 384
RSP_1340 RSP_1340 Enoyl-CoA hydratase/isomerase (NCBI) 67, 384
RSP_1367 RSP_1367 Nicotinate phosphoribosyltransferase (NCBI) 207, 384
RSP_1368 pncA probable pyrazinamidase/nicotinamidase (NCBI) 136, 384
RSP_1379 RSP_1379 Cytosol aminopeptidase (NCBI) 175, 384
RSP_1606 RSP_1606 Putative regulatory protein, GntR family (NCBI) 32, 214
RSP_1607 RSP_1607 Putative regulatory protein, GntR family (NCBI) 77, 214
RSP_1608 RSP_1608 Putative Zn-dependent dehydrogenase (NCBI) 32, 214
RSP_1609 RSP_1609 Putative altronate dehydrogenase (NCBI) 32, 214
RSP_1610 RSP_1610 altronate hydrolase (NCBI) 32, 214
RSP_1754 RSP_1754 hypothetical protein (NCBI) 72, 384
RSP_1893 RSP_1893 Inositol monophosphatase family protein (NCBI) 214, 240
RSP_1926 RSP_1926 tRNA-Dihydrouridine synthase (NCBI) 214, 311
RSP_1983 sqdA Phospholipid/glycerol acyltransferase (NCBI) 293, 384
RSP_2103 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI) 256, 384
RSP_2188 RSP_2188 hypothetical protein (NCBI) 175, 214
RSP_2189 pccB propionyl-CoA carboxylase beta chain (NCBI) 121, 214
RSP_2192 mcmA Methylmalonyl-CoA mutase (NCBI) 65, 384
RSP_2230 RSP_2230 response regulator receiver domain protein (NCBI) 214, 353
RSP_2696 RSP_2696 ABC transporter, fused ATPase and inner membrane subunits (NCBI) 214, 311
RSP_2717 RSP_2717 putative UUP ATPase (NCBI) 214, 311
RSP_2722 cysS Cysteinyl-tRNA synthetase, class Ia (NCBI) 30, 214
RSP_2744 RSP_2744 hypothetical protein (NCBI) 214, 299
RSP_2883 pgm Probable phosphoglucomutase/phosphomannomutase (NCBI) 175, 384
RSP_2908 RSP_2908 hypothetical protein (NCBI) 110, 384
RSP_2909 RSP_2909 Hydrolase arginase family (NCBI) 110, 384
RSP_2915 phoR Probable two-component sensor histidine kinase (NCBI) 213, 214
RSP_3004 RSP_3004 Possible Protein kinase (NCBI) 209, 214
RSP_3102 RSP_3102 putative sec-independent protein translocase protein, TatE (NCBI) 214, 306
RSP_3246 RSP_3246 putative D-alanyl-D-alanine carboxypeptidase (NCBI) 175, 384
RSP_3507 RSP_3507 hypothetical protein (NCBI) 381, 384
RSP_3593 RSP_3593 hypothetical protein (NCBI) 214, 356
RSP_3665 RSP_3665 transcriptional regulator, LuxR family (NCBI) 214, 384
RSP_3728 RSP_3728 putative acyl carrier protein phosphodiesterase (NCBI) 354, 384
RSP_4298 RSP_4298 tRNA-Trp (NCBI) 75, 214
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_3665
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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