Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0068 rpoN2

Sigma-54 factor (RpoN2) (NCBI)

CircVis
Functional Annotations (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0068
(Mouseover regulator name to see its description)

RSP_0068 is regulated by 6 influences and regulates 29 modules.
Regulators for RSP_0068 rpoN2 (6)
Regulator Module Operator
RSP_0032 211 tf
RSP_0068 211 tf
RSP_0071 211 tf
RSP_0032 90 tf
RSP_0068 90 tf
RSP_0071 90 tf

Warning: RSP_0068 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
7900 8.00e+00 CAAAAATcC
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7901 2.30e+01 TtGACAG
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8142 3.60e+02 TtcCGCCagtcTtTTCcct
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8143 1.80e+02 aC.GgccgGc.gcGCcTtcga
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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_0068

RSP_0068 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
Module neighborhood information for RSP_0068

RSP_0068 has total of 35 gene neighbors in modules 90, 211
Gene neighbors (35)
Gene Common Name Description Module membership
RSP_0035 RSP_0035 hypothetical protein (NCBI) 90, 211
RSP_0036 flgA flagellar basal-body P-ring formation protein FlgA (NCBI) 211, 252
RSP_0037 flgM Putative FlgM, negative regulator of flagellin synthesis (NCBI) 90, 352
RSP_0038 RSP_0038 hypothetical protein (NCBI) 90, 179
RSP_0039 RSP_0039 hypothetical protein (NCBI) 90, 211
RSP_0040 fliS putative flagellar protein FliS (NCBI) 90, 211
RSP_0042 cheA3 Chemotaxis histidine protein kinase, CheA3 (NCBI) 90, 352
RSP_0043 cheY6 chemotaxis response regulator, CheY6 (NCBI) 90, 352
RSP_0044 tlpT putative cytoplasmic chemoreceptor, TlpT (NCBI) 90, 352
RSP_0045 slp Slp (NCBI) 90, 211
RSP_0046 cheW4 Chemotaxis protein, CheW4 (NCBI) 90, 198
RSP_0047 cheB2 chemotaxis methylesterase, CheB2 (NCBI) 90, 211
RSP_0048 cheR3 MCP methyltransferase, CheR3 (NCBI) 90, 211
RSP_0049 cheA4 Chemotaxis histidine protein kinase, CheA4 (NCBI) 90, 198
RSP_0062 fliO Flagellar protein FliO (NCBI) 206, 211
RSP_0063 fliP Flagellar transport protein FliP (NCBI) 206, 211
RSP_0065 fliR Flagellar protein FliR (NCBI) 211, 252
RSP_0066 flhB Flagellar protein FlhB (NCBI) 211, 252
RSP_0067 RSP_0067 hypothetical protein (NCBI) 206, 211
RSP_0068 rpoN2 Sigma-54 factor (RpoN2) (NCBI) 90, 211
RSP_0069 fliC Flagellar filament protein (NCBI) 90, 352
RSP_0070 fliD possible flagellar hook-associated protein 2 (filament cap protein) (NCBI) 90, 198
RSP_1582 RSP_1582 Putative sulfate transporter/antisigma-factor antagonist (NCBI) 90, 211
RSP_1583 cheY3 Chemotaxis response regulator, CheY3 (NCBI) 90, 198
RSP_1584 cheA2 Chemotaxis histidine protein kinase (NCBI) 90, 198
RSP_1585 cheW2 Chemotaxis protein, CheW2 (NCBI) 198, 211
RSP_1586 cheW3 Chemotaxis protein, CheW3 (NCBI) 90, 198
RSP_1587 cheR2 Chemotaxis methyltransferase, CheR2 (NCBI) 198, 211
RSP_1588 cheB1 chemotaxis methylesterase, CheB1 (NCBI) 198, 211
RSP_1589 tlpC Transducer-like protein, TlpC (NCBI) 198, 211
RSP_3083 mcpH methyl accepting chemotaxis protein (NCBI) 90, 198
RSP_3302 cheY4 Chemotaxis response regulator, CheY4 (NCBI) 90, 198
RSP_3303 mcpG Putative methyl accepting chemotaxis protein, McpG (NCBI) 90, 211
RSP_3432 RSP_3432 methyl-accepting chemotaxis protein (NCBI) 60, 211
RSP_3708 mcpJ methyl accepting chemotaxis protein (NCBI) 60, 211
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_0068
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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