Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2428 cobT

nicotinate-nucleotide-dimethylbenzimidazolephosphoribosyltransferase (NCBI)

CircVis
Functional Annotations (7)
Function System
NaMN:DMB phosphoribosyltransferase cog/ cog
nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cobT_DBIPRT tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2428
(Mouseover regulator name to see its description)

RSP_2428 is regulated by 16 influences and regulates 0 modules.
Regulators for RSP_2428 cobT (16)
Regulator Module Operator
RSP_2346 33 tf
RSP_2533 33 tf
RSP_2838 33 tf
RSP_2889 33 tf
RSP_2950 33 tf
RSP_3665 33 tf
RSP_0601 318 tf
RSP_1231 318 tf
RSP_1550 318 tf
RSP_1776 318 tf
RSP_2572 318 tf
RSP_2719 318 tf
RSP_2838 318 tf
RSP_2840 318 tf
RSP_2922 318 tf
RSP_3309 318 tf

Warning: RSP_2428 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
7786 1.60e-06 CcgGAtcccgCtgGcaaCcGcAAG
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7787 9.60e-03 cCactgcCGCTcCgCgatacCGga
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8348 7.90e-05 caTAtCaaGAaaccACacCaAAGT
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8349 6.70e-02 aCCactgCcGtTtgcCGA
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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_2428

RSP_2428 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
NaMN:DMB phosphoribosyltransferase cog/ cog
nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cobT_DBIPRT tigr/ tigrfam
Module neighborhood information for RSP_2428

RSP_2428 has total of 33 gene neighbors in modules 33, 318
Gene neighbors (33)
Gene Common Name Description Module membership
RSP_0650 RSP_0650 Probable transglycosylase (NCBI) 7, 33
RSP_0651 RSP_0651 Putative inositol monophosphatase protein (NCBI) 33, 130
RSP_0653 RSP_0653 UDP-glucose 6-dehydrogenase (NCBI) 33, 374
RSP_0654 RSP_0654 possible transporter, DMT superfamily (NCBI) 33, 242
RSP_0749 RSP_0749 hypothetical protein (NCBI) 318, 354
RSP_1030 RSP_1030 putative pfkB family carbohydrate kinase (NCBI) 110, 318
RSP_1216 rbsK putative RbsK, Carbohydrate kinase, ribokinase family (NCBI) 36, 318
RSP_1217 RSP_1217 putative Malic oxidoreductase; Pta, Phosphotransacetylase (NCBI) 36, 318
RSP_2427 cobV putative Cobalamin (5'-phosphate) synthase (NCBI) 33, 256
RSP_2428 cobT nicotinate-nucleotide-dimethylbenzimidazolephosphoribosyltransferase (NCBI) 33, 318
RSP_2726 RSP_2726 multidrug/metabolite efflux pump, Major facilitator superfamily (MFS) (NCBI) 33, 51
RSP_2727 RSP_2727 probable 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase (NCBI) 33, 273
RSP_2728 RSP_2728 Phospholipase/Carboxylesterase (NCBI) 33, 51
RSP_2786 HPRT Hypoxanthine-guanine phosphoribosyltransferase (NCBI) 281, 318
RSP_2787 RSP_2787 hypothetical protein (NCBI) 108, 318
RSP_2833 cinA Putative competence-damaged inducible protein (NCBI) 100, 318
RSP_2834 pgpA Putative Phosphatidylglycerophosphatase A (NCBI) 100, 318
RSP_2836 nifR3 tRNA-dihydrouridine synthase, nifR3 (NCBI) 240, 318
RSP_2837 ntrB Nitrogen regulation protein, NtrB signal transduction histidine kinase (NCBI) 99, 318
RSP_2838 ntrC nitrogen metabolism transcriptional regulator, NtrC (NCBI) 259, 318
RSP_2839 ntrY Nitrogen regulation protein, NtrY, Signal transduction histidine kinase (NCBI) 99, 318
RSP_2840 ntrX Nitrogen assimilation transcriptional regulator, NtrX (NCBI) 259, 318
RSP_2901 RSP_2901 putative permease (NCBI) 223, 318
RSP_3509 expE1 Hemolysin-type calcium-binding region, RTX (NCBI) 33, 239
RSP_3510 RSP_3510 hypothetical protein (NCBI) 33, 239
RSP_3512 RSP_3512 periplasmic sensor signal transduction histidine kinase (NCBI) 33, 239
RSP_6011 RSP_6011 Putative transposase protein (NCBI) 33, 156
RSP_6013 RSP_6013 hypothetical protein (NCBI) 33, 243
RSP_6022 RSP_6022 hypothetical protein (NCBI) 33, 205
RSP_6152 RSP_6152 hypothetical protein (NCBI) 33, 190
RSP_6177 gpFI Major tail sheath protein FI (NCBI) 33, 364
RSP_6193 RSP_6193 hypothetical protein (NCBI) 33, 243
RSP_6229 RSP_6229 hypothetical protein (NCBI) 33, 266
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_2428
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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