Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1449

Putative transcriptional regulator of sugar metabolism (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1449
(Mouseover regulator name to see its description)

RSP_1449 is regulated by 15 influences and regulates 2 modules.
Regulators for RSP_1449 (15)
Regulator Module Operator
RSP_0641 155 tf
RSP_1077 155 tf
RSP_1164 155 tf
RSP_1274 155 tf
RSP_1449 155 tf
RSP_2362 155 tf
RSP_2494 155 tf
RSP_3667 155 tf
RSP_3680 155 tf
RSP_0185 307 tf
RSP_1077 307 tf
RSP_1231 307 tf
RSP_1660 307 tf
RSP_1776 307 tf
RSP_1790 307 tf

Warning: RSP_1449 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
8030 1.10e-05 gTGAtAGTTTcG
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8031 1.40e-03 CgaacGCTGcCatAattCaCtGaa
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8328 4.80e-12 CTCGCcCcattccGCG.AatgaCa
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8329 3.30e-09 atCCccgcCagatgtggAAgA
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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_1449

RSP_1449 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_1449

RSP_1449 has total of 39 gene neighbors in modules 155, 307
Gene neighbors (39)
Gene Common Name Description Module membership
RSP_0302 ureG Urease accessory protein G (NCBI) 175, 307
RSP_0303 ureF Urease accessory protein UreF (NCBI) 175, 307
RSP_0304 ureE urease accessory protein UreE (NCBI) 175, 307
RSP_0305 RSP_0305 hypothetical protein (NCBI) 175, 307
RSP_0306 RSP_0306 Class I diheme cytochrome c (NCBI) 175, 307
RSP_1263 RSP_1263 hypothetical protein (NCBI) 84, 307
RSP_1264 RSP_1264 hypothetical protein (NCBI) 84, 307
RSP_1265 kdpA Potassium-transporting P-type ATPase, A chain, KdpA (NCBI) 84, 307
RSP_1266 kdpB Potassium-transporting P-type ATPase, B chain, KdpB (NCBI) 84, 307
RSP_1267 kdpC Potassium-transporting P-type ATPase C chain, kdpC (NCBI) 84, 307
RSP_1268 kdpD Osmosensitive K+ channel histidine kinase (NCBI) 84, 307
RSP_1269 kdpE two component transcriptional regulator, winged helix family (NCBI) 84, 307
RSP_1444 RSP_1444 ABC sugar transporter, inner membrane subunit (NCBI) 155, 325
RSP_1449 RSP_1449 Putative transcriptional regulator of sugar metabolism (NCBI) 155, 307
RSP_1953 RSP_1953 Transcriptional regulator, CRP/FNR family (NCBI) 155, 325
RSP_1954 RSP_1954 hypothetical protein (NCBI) 155, 304
RSP_2186 RSP_2186 Transcriptional Regulator, MerR family (NCBI) 238, 307
RSP_2187 RSP_2187 multidrug efflux pump, Major Facilitator Superfamily ( MFS) (NCBI) 19, 307
RSP_2599 phoB Phosphate regulon transcriptional regulator, PhoR (NCBI) 84, 155
RSP_2600 phoU phosphate transport system regulatory protein (NCBI) 155, 306
RSP_2601 pstB ABC phosphate transporter, ATPase subunit PstB (NCBI) 155, 306
RSP_2602 pstA ABC phosphate transporter, inner membrane subunit PstA (NCBI) 155, 306
RSP_2603 pstC ABC phosphate transporter, inner membrane subunit PstC (NCBI) 155, 306
RSP_2604 pstS ABC phosphate transporter, periplasmic phosphate-binding protein (NCBI) 155, 306
RSP_2872 aglF ABC alpha-glucoside transporter, inner membrane subunit AglF (NCBI) 281, 307
RSP_2873 aglE ABC alpha-glucoside transporter, perplasmic substrate-binding protein (NCBI) 73, 307
RSP_2988 RSP_2988 Pirin-related protein (NCBI) 155, 238
RSP_2989 RSP_2989 hypothetical protein (NCBI) 11, 155
RSP_2994 RSP_2994 hypothetical protein (NCBI) 155, 355
RSP_3046 dorC DMSO/TMAO pentaheme cytochrome c subunit (NCBI) 155, 308
RSP_3047 dorB DMSO-membrane protein (NCBI) 155, 308
RSP_3048 dorA DMSO/TMAO-reductase (NCBI) 155, 308
RSP_3049 moeA Molybdenum cofactor biosynthesis protein (NCBI) 155, 308
RSP_3068 RSP_3068 hypothetical protein (NCBI) 38, 307
RSP_3624 RSP_3624 hypothetical protein (NCBI) 235, 307
RSP_3666 RSP_3666 putative membrane protein (NCBI) 115, 155
RSP_3667 RSP_3667 transcriptional regulator, AraC family with Parallel beta-helix repeat (NCBI) 115, 155
RSP_3669 RSP_3669 hypothetical protein (NCBI) 115, 155
RSP_3792 RSP_3792 hypothetical protein (NCBI) 307, 346
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_1449
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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