Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2867 rpoN4

Sigma-54 factor family protein (NCBI)

CircVis
Functional Annotations (8)
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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2867
(Mouseover regulator name to see its description)

RSP_2867 is regulated by 18 influences and regulates 46 modules.
Regulators for RSP_2867 rpoN4 (18)
Regulator Module Operator
RSP_0282 292 tf
RSP_0607 292 tf
RSP_1014 292 tf
RSP_1231 292 tf
RSP_1660 292 tf
RSP_1785 292 tf
RSP_1790 292 tf
RSP_2867 292 tf
RSP_3064 292 tf
RSP_3238 292 tf
RSP_3464 292 tf
RSP_1014 282 tf
RSP_1231 282 tf
RSP_2610 282 tf
RSP_2867 282 tf
RSP_3322 282 tf
RSP_3464 282 tf
RSP_3684 282 tf

Warning: RSP_2867 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
8278 1.60e+02 aAAttgtcAAT
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8279 4.00e+03 AACccGAtcca
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8298 6.00e+02 cCgaGaTCGAG
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8299 4.30e+02 agAagaagaagCgcaacCaGa
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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_2867

RSP_2867 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
Module neighborhood information for RSP_2867

RSP_2867 has total of 47 gene neighbors in modules 282, 292
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0410 RSP_0410 sensor diguanylate cyclase (GGDEF) (NCBI) 249, 282
RSP_0494 hypF hydrogenase maturation factor F (NCBI) 292, 337
RSP_1115 RSP_1115 hypothetical protein (NCBI) 246, 292
RSP_1118 RSP_1118 group 1 glycosyltransferase (NCBI) 246, 292
RSP_1450 RSP_1450 Inositol monophosphatase family protein (NCBI) 105, 292
RSP_1458 RSP_1458 Putative DNA repair enzyme (NCBI) 244, 282
RSP_1501 RSP_1501 Antisigma-factor antagonist (STAS) domain protein (NCBI) 74, 292
RSP_1509 RSP_1509 Glycoprotease (M22) metalloprotease (NCBI) 292, 300
RSP_1661 RSP_1661 hypothetical protein (NCBI) 292, 300
RSP_1774 RSP_1774 Putative glucose dehydrogenase B (NCBI) 138, 282
RSP_1816 RSP_1816 Mg chelatase-related protein (NCBI) 238, 282
RSP_1923 bioB Biotin synthase (NCBI) 62, 292
RSP_1981 RSP_1981 Deoxyribodipyrimidine photolyase (NCBI) 153, 282
RSP_2061 RSP_2061 hypothetical protein (NCBI) 292, 379
RSP_2072 RSP_2072 Putative Phage-related Holin protein (NCBI) 138, 282
RSP_2315 RSP_2315 hypothetical protein (NCBI) 105, 292
RSP_2501 RSP_2501 hypothetical protein (NCBI) 238, 292
RSP_2672 RSP_2672 hypothetical protein (NCBI) 38, 282
RSP_2732 RSP_2732 Major facilitator superfamily (MFS) transporter (NCBI) 68, 292
RSP_2759 RSP_2759 hypothetical protein (NCBI) 246, 282
RSP_2761 RSP_2761 putative P2-like prophage tail protein X (NCBI) 246, 282
RSP_2789 RSP_2789 hypothetical protein (NCBI) 236, 282
RSP_2867 rpoN4 Sigma-54 factor family protein (NCBI) 282, 292
RSP_3030 RSP_3030 ABC peptide/opine transporter, inner membrane subunit (NCBI) 193, 282
RSP_3032 RSP_3032 ABC peptide/opine transporter, ATPase subunit (NCBI) 193, 282
RSP_3033 RSP_3033 ABC peptide/opine transporter, ATPase subunit (NCBI) 193, 282
RSP_3034 RSP_3034 ABC peptide/opine transporter, periplasmic substrate-binding protein (NCBI) 193, 282
RSP_3064 RSP_3064 transcriptional regulator, DeoR family (NCBI) 235, 292
RSP_3108 RSP_3108 Putative methyl accepting chemotaxis protein (NCBI) 246, 292
RSP_3114 RSP_3114 hypothetical protein (NCBI) 77, 282
RSP_3128 RSP_3128 hypothetical protein (NCBI) 292, 337
RSP_3135 RSP_3135 ppkA-related protein (NCBI) 244, 292
RSP_3258 RSP_3258 ABC peptide transporter, inner membrane subunit (NCBI) 236, 282
RSP_3358 gpX Phage tail component protein X (NCBI) 282, 304
RSP_3359 gpD Phage tail protein D (NCBI) 191, 282
RSP_3471 RSP_3471 hypothetical protein (NCBI) 147, 292
RSP_3516 RSP_3516 ABC polyamine/opine transporter, ATPase subunit (NCBI) 31, 282
RSP_3519 RSP_3519 putative proline racemase (NCBI) 282, 331
RSP_3580 gvpJ Gas vesicle protein GVPa (NCBI) 253, 282
RSP_3613 RSP_3613 Glycosyltransferase (NCBI) 238, 292
RSP_3654 RSP_3654 None 193, 292
RSP_3743 speB1 putative agmatinase (NCBI) 61, 292
RSP_3746 RSP_3746 hypothetical protein (NCBI) 61, 292
RSP_3764 RSP_3764 hypothetical protein (NCBI) 292, 347
RSP_3780 RSP_3780 hypothetical protein (NCBI) 147, 292
RSP_3789 RSP_3789 hypothetical protein (NCBI) 88, 292
RSP_3796 RSP_3796 hypothetical protein (NCBI) 253, 282
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_2867
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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