Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2610

trancriptional regulator, MerR family (NCBI)

CircVis
Functional Annotations (4)
Function System
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2610
(Mouseover regulator name to see its description)

RSP_2610 is regulated by 27 influences and regulates 50 modules.
Regulators for RSP_2610 (27)
Regulator Module Operator
RSP_0087 127 tf
RSP_0316 127 tf
RSP_0402 127 tf
RSP_0415 127 tf
RSP_0698 127 tf
RSP_0755 127 tf
RSP_1550 127 tf
RSP_1606 127 tf
RSP_1871 127 tf
RSP_1890 127 tf
RSP_2425 127 tf
RSP_2591 127 tf
RSP_2610 127 tf
RSP_3124 127 tf
RSP_0087 81 tf
RSP_0316 81 tf
RSP_0958 81 tf
RSP_1139 81 tf
RSP_1243 81 tf
RSP_1550 81 tf
RSP_1606 81 tf
RSP_1663 81 tf
RSP_1866 81 tf
RSP_1890 81 tf
RSP_2610 81 tf
RSP_3238 81 tf
RSP_3606 81 tf

Warning: RSP_2610 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
7882 9.70e-01 cAtg.Gc.gaacacagCgGgc
Loader icon
7883 2.30e+01 taAcAgGaaAc
Loader icon
7974 6.10e+02 ATatTTGc.CagAGtGaAaGCG
Loader icon
7975 4.30e+03 tTTTTCA
Loader icon
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_2610

RSP_2610 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2610

RSP_2610 has total of 52 gene neighbors in modules 81, 127
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0087 RSP_0087 two component transcriptional regulator, LuxR (NCBI) 70, 81
RSP_0359 cbbI Ribose-5-phosphate isomerase (NCBI) 127, 372
RSP_0453 RSP_0453 hypothetical protein (NCBI) 52, 81
RSP_0683 RSP_0683 hypothetical protein (NCBI) 81, 127
RSP_0717 RSP_0717 hypothetical protein (NCBI) 48, 81
RSP_0758 RSP_0758 Lumazine-binding protein (NCBI) 127, 207
RSP_0762 RSP_0762 transcriptional regulator, XRE family (NCBI) 127, 162
RSP_0798 RSP_0798 Neutral zinc metallopeptidases (NCBI) 52, 81
RSP_0999 RSP_0999 hypothetical protein (NCBI) 127, 162
RSP_1001 RSP_1001 hypothetical protein (NCBI) 127, 341
RSP_1007 RSP_1007 hypothetical protein (NCBI) 10, 127
RSP_1029 RSP_1029 possible Histidine triad (HIT) protein (NCBI) 127, 200
RSP_1070 RSP_1070 hypothetical protein (NCBI) 81, 162
RSP_1126 rnr Exoribonuclease R (NCBI) 127, 262
RSP_1261 blrB blue-light receptor of the BLUF-family (NCBI) 81, 162
RSP_1356 RSP_1356 hypothetical protein (NCBI) 81, 92
RSP_1385 RSP_1385 hypothetical protein (NCBI) 81, 127
RSP_1397 RSP_1397 Glutathione S-transferase (NCBI) 52, 81
RSP_1430 RSP_1430 hypothetical protein (NCBI) 127, 223
RSP_1493 RSP_1493 Amidase (NCBI) 81, 278
RSP_1550 RSP_1550 regulatory proteins, IclR family (NCBI) 127, 341
RSP_1663 RSP_1663 putative transcriptional regulator, LacI family (NCBI) 81, 126
RSP_1665 RSP_1665 putative RhtB family transporter (NCBI) 81, 85
RSP_1666 LytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 81, 85
RSP_1812 RSP_1812 hypothetical protein (NCBI) 81, 221
RSP_1868 RSP_1868 serine-pyruvate aminotransferase (NCBI) 10, 127
RSP_2120 RSP_2120 putative D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase (NCBI) 10, 127
RSP_2139 RSP_2139 hypothetical protein (NCBI) 127, 162
RSP_2173 RSP_2173 hypothetical protein (NCBI) 127, 223
RSP_2174 RSP_2174 Putative ABC transporter, inner membrane subunit (NCBI) 127, 223
RSP_2216 ilvE Aminotransferase, class IV (NCBI) 127, 207
RSP_2309 RSP_2309 hypothetical protein (NCBI) 127, 262
RSP_2399 RSP_2399 ABC putrescine transporter, inner membrane subunit (NCBI) 127, 291
RSP_2400 RSP_2400 ABC putrescine transporter, ATPase subunit (NCBI) 127, 162
RSP_2401 RSP_2401 putative 6-aminohexanoate-cyclic-dimer hydrolase (NCBI) 81, 127
RSP_2610 RSP_2610 trancriptional regulator, MerR family (NCBI) 81, 127
RSP_2611 ihfA Histone-like DNA-binding protein (IHF) (NCBI) 81, 127
RSP_2695 RSP_2695 Possible peptidoglycan binding protein (NCBI) 81, 207
RSP_2772 ftsJ 23S rRNA methylase (NCBI) 127, 308
RSP_2775 lpxD UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase (NCBI) 127, 223
RSP_2846 RSP_2846 putative 3-hydroxyisobutyrate dehydrogenase (NCBI) 81, 207
RSP_2862 RSP_2862 Glycine/D-amino acid oxidases (deaminating) (NCBI) 127, 207
RSP_2886 glgC ADP-glucose pyrophosphorylase (NCBI) 16, 81
RSP_2900 RSP_2900 Predicted permease (NCBI) 127, 223
RSP_2947 RSP_2947 Glutamate racemase (NCBI) 127, 223
RSP_2954 RSP_2954 hypothetical protein (NCBI) 81, 162
RSP_2955 RSP_2955 hypothetical protein (NCBI) 81, 162
RSP_2969 RSP_2969 hypothetical protein (NCBI) 127, 207
RSP_3069 RSP_3069 NADPH-dependent FMN reductase (NCBI) 81, 207
RSP_3563 RSP_3563 putative FAD-dependent glycerol-3-phosphate dehydrogenase protein (NCBI) 127, 207
RSP_3589 ihfB Integration host factor beta-subunit (NCBI) 48, 81
RSP_3730 RSP_3730 putative glutathione S-transferase (NCBI) 81, 207
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_2610
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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