Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3418

transcriptional regulator, AraC family (NCBI)

CircVis
Functional Annotations (5)
Function System
AraC-type DNA-binding domain-containing proteins 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_3418
(Mouseover regulator name to see its description)

RSP_3418 is regulated by 11 influences and regulates 13 modules.
Regulators for RSP_3418 (11)
Regulator Module Operator
RSP_0611 340 tf
RSP_0623 340 tf
RSP_1191 340 tf
RSP_1286 340 tf
RSP_2850 340 tf
RSP_3418 340 tf
RSP_3680 340 tf
RSP_0386 146 tf
RSP_1191 146 tf
RSP_2572 146 tf
RSP_3418 146 tf

Warning: RSP_3418 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
8012 3.20e+03 ATCTCg
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8013 5.00e+04 AATGCTGC
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8382 1.00e+03 gCtgGaacTtC.agAtcgG
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8383 4.90e+03 t.TTTcagAagGacGAAata
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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_3418

RSP_3418 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
AraC-type DNA-binding domain-containing proteins 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
Module neighborhood information for RSP_3418

RSP_3418 has total of 38 gene neighbors in modules 146, 340
Gene neighbors (38)
Gene Common Name Description Module membership
RSP_0008 RSP_0008 possible transporter, DME family, DMT superfamily (NCBI) 323, 340
RSP_0202 RSP_0202 putative membrane protein (NCBI) 221, 340
RSP_0409 RSP_0409 hypothetical protein (NCBI) 134, 146
RSP_0551 RSP_0551 putative thymidylate kinase (NCBI) 234, 340
RSP_0560 priA Probable pimosomal protein N' (NCBI) 54, 340
RSP_0608 RSP_0608 hypothetical protein (NCBI) 146, 216
RSP_0609 RSP_0609 hypothetical protein (NCBI) 146, 304
RSP_0619 RSP_0619 hypothetical protein (NCBI) 146, 188
RSP_0685 RSP_0685 Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI) 209, 340
RSP_0937 RSP_0937 Alpha amylase, catalytic subdomain (NCBI) 40, 340
RSP_1057 merA1 Putative mercuric reductase protein (NCBI) 134, 340
RSP_1074 uvrC Excinuclease ABC, C subunit (NCBI) 208, 340
RSP_1275 RSP_1275 Crp-Fnr family transciptional regulator (NCBI) 215, 340
RSP_1286 cbbR RuBisCO operon transcriptional regulator, CbbR (NCBI) 54, 340
RSP_1321 fliR Flagellar biosynthesis pathway, component FliR (NCBI) 146, 340
RSP_1364 RSP_1364 hypothetical protein (NCBI) 146, 340
RSP_1540 RSP_1540 Predicted secreted hydrolase (NCBI) 125, 146
RSP_1541 RSP_1541 Putative ABC transporter, fused inner membrane subunits (NCBI) 125, 146
RSP_2080 RSP_2080 Putative Tyrosine recombinase (NCBI) 251, 340
RSP_2102 RSP_2102 hypothetical protein (NCBI) 110, 146
RSP_2223 RSP_2223 AcrB/AcrD/AcrF multidrug efflux pump (NCBI) 171, 340
RSP_2240 RSP_2240 hypothetical protein (NCBI) 213, 340
RSP_2250 RSP_2250 hypothetical protein (NCBI) 44, 340
RSP_2302 RSP_2302 putative low specificity L-threonine aldolase (NCBI) 54, 146
RSP_2390 acuC1 putative Acetoin utilization protein (NCBI) 126, 340
RSP_2650 RSP_2650 hypothetical protein (NCBI) 121, 340
RSP_2678 RSP_2678 hypothetical protein (NCBI) 215, 340
RSP_2850 mfd transcription-repair coupling factor (helicase) (NCBI) 54, 340
RSP_2884 glgX glycogen debranching enzyme (NCBI) 233, 340
RSP_3105 RSP_3105 PAS sensor protein (NCBI) 83, 340
RSP_3200 RSP_3200 Molecular chaperone, DnaK (NCBI) 146, 356
RSP_3250 RSP_3250 ABC peptide transporter, inner membrane subunit (NCBI) 267, 340
RSP_3379 RSP_3379 hypothetical protein (NCBI) 133, 146
RSP_3390 RSP_3390 ABC Fe3+-siderophores transporter, ATPase subunit (NCBI) 146, 235
RSP_3418 RSP_3418 transcriptional regulator, AraC family (NCBI) 146, 340
RSP_3431 RSP_3431 periplasmic sensor signal transduction histidine kinase (NCBI) 146, 158
RSP_3610 RSP_3610 hypothetical protein (NCBI) 177, 340
RSP_3779 RSP_3779 hypothetical protein (NCBI) 94, 146
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_3418
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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