Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2171 metR

transcriptional regulator, LysR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2171
(Mouseover regulator name to see its description)

RSP_2171 is regulated by 27 influences and regulates 25 modules.
Regulators for RSP_2171 metR (27)
Regulator Module Operator
RSP_0511 67 tf
RSP_0760 67 tf
RSP_1191 67 tf
RSP_1225 67 tf
RSP_2130 67 tf
RSP_2171 67 tf
RSP_2182 67 tf
RSP_2533 67 tf
RSP_2681 67 tf
RSP_2730 67 tf
RSP_2853 67 tf
RSP_2939 67 tf
RSP_3022 67 tf
RSP_0327 259 tf
RSP_0402 259 tf
RSP_0507 259 tf
RSP_0547 259 tf
RSP_0623 259 tf
RSP_0755 259 tf
RSP_1590 259 tf
RSP_2171 259 tf
RSP_2346 259 tf
RSP_2591 259 tf
RSP_2838 259 tf
RSP_2840 259 tf
RSP_2950 259 tf
RSP_3324 259 tf

Warning: RSP_2171 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
7854 8.00e+02 atgCtCAAGAt
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7855 3.20e+03 AAAtATGA
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8236 5.90e-06 tgaAaatAtGCaa
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8237 9.70e-07 TCaatatgaTcTtattCaTTcaaA
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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_2171

RSP_2171 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2171

RSP_2171 has total of 56 gene neighbors in modules 67, 259
Gene neighbors (56)
Gene Common Name Description Module membership
RSP_0085 RSP_0085 multisensor hybrid histidine kinase (NCBI) 60, 259
RSP_0086 RSP_0086 hypothetical protein (NCBI) 60, 259
RSP_0331 RSP_0331 hypothetical protein (NCBI) 259, 344
RSP_0332 RSP_0332 possible cellulose synthase (NCBI) 240, 259
RSP_0333 RSP_0333 possible cellulose synthase (NCBI) 259, 344
RSP_0334 RSP_0334 hypothetical protein (NCBI) 59, 259
RSP_0371 RSP_0371 ABC basic amino acid transporter, ATPase subunit (NCBI) 67, 114
RSP_0372 RSP_0372 ABC basic amino acid transporter, solute-binding protein (NCBI) 67, 114
RSP_0375 RSP_0375 probable glutamine synthetase (NCBI) 65, 67
RSP_0377 RSP_0377 probable glutamine synthetase (NCBI) 110, 259
RSP_0378 RSP_0378 hypothetical protein (NCBI) 110, 259
RSP_0402 RSP_0402 transcriptional regulator, TetR family (NCBI) 26, 259
RSP_0463 RSP_0463 cation efflux transporter, CDF family (NCBI) 22, 67
RSP_0565 RSP_0565 putative phosphatidylcholine synthase (NCBI) 67, 108
RSP_0804 DppD ABC dipeptide transporter, ATPase subunit DppD (NCBI) 67, 114
RSP_0805 DppC ABC dipeptide transporter, inner membrane subunit DppC (NCBI) 57, 67
RSP_0809 RSP_0809 hypothetical protein (NCBI) 67, 207
RSP_0973 RSP_0973 MaoC family protein (NCBI) 67, 118
RSP_1144 Gst Glutathione S-transferase (NCBI) 67, 245
RSP_1145 RSP_1145 Peptidoglycan transglycosylase (NCBI) 67, 254
RSP_1166 mutT NTP pyrophosphohydrolase (NCBI) 259, 374
RSP_1182 RSP_1182 putative outer membrane protein (NCBI) 110, 259
RSP_1183 RSP_1183 hypothetical protein (NCBI) 110, 259
RSP_1186 RSP_1186 hypothetical protein (NCBI) 59, 67
RSP_1340 RSP_1340 Enoyl-CoA hydratase/isomerase (NCBI) 67, 384
RSP_1422 RSP_1422 ParB-like nuclease (NCBI) 259, 293
RSP_1853 TrkH2 potassium uptake transporter, transmembrane component, TrkH (NCBI) 29, 67
RSP_1854 trkH3 potassium uptake transporter, transmembrane component, TrkH (NCBI) 67, 288
RSP_2171 metR transcriptional regulator, LysR family (NCBI) 67, 259
RSP_2205 RSP_2205 hypothetical protein (NCBI) 67, 234
RSP_2206 RSP_2206 hypothetical protein (NCBI) 67, 234
RSP_2207 deoD purine nucleoside phosphorylase (NCBI) 67, 110
RSP_2208 RSP_2208 ABC sugar transporter, inner membrane subunit (NCBI) 67, 174
RSP_2209 RSP_2209 ABC sugar transporter, inner membrane subunit (NCBI) 67, 174
RSP_2211 RSP_2211 ABC transporter, periplasmic substrate-binding protein (NCBI) 67, 70
RSP_2332 RSP_2332 hypothetical protein (NCBI) 67, 72
RSP_2541 tatC twin-arginine translocation system protein, TatC (NCBI) 67, 291
RSP_2592 RSP_2592 hypothetical protein (NCBI) 26, 259
RSP_2593 flhS hybrid histidine kinase (NCBI) 26, 259
RSP_2594 RSP_2594 hypothetical protein (NCBI) 26, 259
RSP_2595 RSP_2595 hypothetical protein (NCBI) 26, 259
RSP_2730 RSP_2730 Transcriptional regulator, ArsR family (NCBI) 67, 95
RSP_2838 ntrC nitrogen metabolism transcriptional regulator, NtrC (NCBI) 259, 318
RSP_2840 ntrX Nitrogen assimilation transcriptional regulator, NtrX (NCBI) 259, 318
RSP_2939 RSP_2939 Predicted transcriptional regulator containing the HTH domain (NCBI) 67, 174
RSP_2941 RSP_2941 Putative Glycoside hydrolase (NCBI) 221, 259
RSP_3216 RSP_3216 putative DNA repair exonuclease (NCBI) 20, 67
RSP_3262 RSP_3262 Putative thioesterase (NCBI) 259, 372
RSP_3313 RSP_3313 possible phage integrase family protein (NCBI) 67, 112
RSP_3330 sac1 Putative sodium/sulfate transporter, DASS family (NCBI) 67, 375
RSP_3367 RSP_3367 hypothetical protein (NCBI) 67, 145
RSP_3731 RSP_3731 transcriptional regulator, DeoR family (NCBI) 259, 353
RSP_3733 RSP_3733 ABC sugar transporter, fused ATPase domains (NCBI) 259, 353
RSP_3736 RSP_3736 hypothetical protein (NCBI) 259, 353
RSP_3739 RSP_3739 deoxyribose phosphate aldolase (NCBI) 259, 353
RSP_3808 RSP_3808 hypothetical protein (NCBI) 67, 114
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.

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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
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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