Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0616

transcriptional regulator, AraC family (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
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_0616
(Mouseover regulator name to see its description)

RSP_0616 is regulated by 23 influences and regulates 6 modules.
Regulators for RSP_0616 (23)
Regulator Module Operator
RSP_1014 83 tf
RSP_1077 83 tf
RSP_1790 83 tf
RSP_1915 83 tf
RSP_2351 83 tf
RSP_2965 83 tf
RSP_3001 83 tf
RSP_0386 88 tf
RSP_0616 88 tf
RSP_0722 88 tf
RSP_0760 88 tf
RSP_1077 88 tf
RSP_1660 88 tf
RSP_1663 88 tf
RSP_1669 88 tf
RSP_1890 88 tf
RSP_2494 88 tf
RSP_3317 88 tf
RSP_3341 88 tf
RSP_3464 88 tf
RSP_3505 88 tf
RSP_3684 88 tf
RSP_3694 88 tf

Warning: RSP_0616 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
7886 5.00e+04 TATGAA
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7887 9.30e+04 TgacGAGGt.CgtGAGgtagC
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7896 9.10e+02 ATctgCAtGaA
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7897 7.60e+02 Gaa.AtCTtaTCGCt
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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_0616

RSP_0616 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
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
Module neighborhood information for RSP_0616

RSP_0616 has total of 37 gene neighbors in modules 83, 88
Gene neighbors (37)
Gene Common Name Description Module membership
RSP_0139 RSP_0139 Ribosomal protein S6 (NCBI) 83, 196
RSP_0176 RSP_0176 Dihydroxyacid dehydratase/phosphogluconate dehydratase (NCBI) 83, 242
RSP_0187 RSP_0187 Dihydroorotate dehydrogenase (NCBI) 83, 244
RSP_0227 RSP_0227 hypothetical protein (NCBI) 88, 189
RSP_0229 RSP_0229 multidrug efflux pump, MF Superfamily (NCBI) 88, 188
RSP_0492 hupU hydrogenase small subunit (NCBI) 83, 133
RSP_0616 RSP_0616 transcriptional regulator, AraC family (NCBI) 83, 88
RSP_0666 RSP_0666 Probable cell cycle protein (NCBI) 88, 326
RSP_0858 RSP_0858 Putative transporter, RhaT family, DMT superfamily (NCBI) 59, 88
RSP_1184 RSP_1184 ribonuclease BN (NCBI) 83, 242
RSP_1650 RSP_1650 hypothetical protein (NCBI) 83, 313
RSP_1655 RSP_1655 hypothetical protein (NCBI) 61, 83
RSP_1660 RSP_1660 putative ParB-like nuclease (NCBI) 88, 380
RSP_1915 RSP_1915 Transcriptional regulator, LysR family (NCBI) 83, 101
RSP_2352 RSP_2352 putative terminase large subunit / phage terminase (NCBI) 74, 83
RSP_2353 RSP_2353 hypothetical protein (NCBI) 74, 83
RSP_2354 RSP_2354 hypothetical protein (NCBI) 23, 83
RSP_2745 RSP_2745 hypothetical protein (NCBI) 22, 83
RSP_2765 RSP_2765 hypothetical protein (NCBI) 88, 285
RSP_3017 RSP_3017 nitrilotriacetate monooxygenase (NCBI) 38, 83
RSP_3026 RSP_3026 Transcriptional regulator, MocR family (NCBI) 83, 168
RSP_3086 RSP_3086 periplasmic sensor signal transduction histidine kinase (NCBI) 83, 176
RSP_3105 RSP_3105 PAS sensor protein (NCBI) 83, 340
RSP_3130 RSP_3130 Putative serine protease (NCBI) 83, 244
RSP_3136 RSP_3136 hypothetical protein (NCBI) 88, 130
RSP_3152 RSP_3152 ABC nitrate/sulfonate/bicarbonate transporter family, periplasmic substrate-binding protein (NCBI) 88, 105
RSP_3388 RSP_3388 putative Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase ttuC (NCBI) 83, 220
RSP_3393 RSP_3393 ABC opine/polyamine transporter, inner membrane subunit (NCBI) 77, 88
RSP_3395 RSP_3395 ABC opine/polyamine transporter, inner membrane subunit (NCBI) 88, 170
RSP_3396 RSP_3396 ABC opine/polyamine transporter, ATPase subunit (NCBI) 88, 170
RSP_3399 RSP_3399 carbon-nitrogen hydrolase family protein (NCBI) 88, 170
RSP_3670 RSP_3670 putative oxidoreductase myo-inositol 2-dehydrogenase (NCBI) 88, 105
RSP_3671 RSP_3671 putative D-tagatose 3-epimerase (NCBI) 88, 115
RSP_3672 RSP_3672 ABC sugar transporter, inner membrane subunit (NCBI) 88, 115
RSP_3673 RSP_3673 ABC sugar transporter, inner membrane subunit (NCBI) 88, 115
RSP_3689 yphD ABC sugar transporter, inner membrane subunit (NCBI) 57, 88
RSP_3789 RSP_3789 hypothetical protein (NCBI) 88, 292
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_0616
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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