Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2907 prfA

peptide chain release factor 1 (NCBI)

CircVis
Functional Annotations (5)
Function System
Protein chain release factor A cog/ cog
cytoplasm go/ cellular_component
translational termination go/ biological_process
translation release factor activity, codon specific go/ molecular_function
prfA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2907
(Mouseover regulator name to see its description)

RSP_2907 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_2907 prfA (18)
Regulator Module Operator
RSP_0316 178 tf
RSP_1040 178 tf
RSP_1139 178 tf
RSP_1486 178 tf
RSP_2410 178 tf
RSP_2853 178 tf
RSP_3665 178 tf
RSP_0443 156 tf
RSP_0728 156 tf
RSP_0755 156 tf
RSP_0774 156 tf
RSP_0927 156 tf
RSP_1164 156 tf
RSP_1890 156 tf
RSP_2026 156 tf
RSP_2922 156 tf
RSP_3203 156 tf
RSP_3341 156 tf

Warning: RSP_2907 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
8032 2.20e-46 actctGccCAAATATCCtCgGGGG
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8033 4.60e-28 CgGGGGGCaGacAGCCCCCcG
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8076 1.10e-01 AcaatCagCagaAaagc
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8077 7.90e-01 AaaaccGgataTTaacccTTttG
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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_2907

RSP_2907 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Protein chain release factor A cog/ cog
cytoplasm go/ cellular_component
translational termination go/ biological_process
translation release factor activity, codon specific go/ molecular_function
prfA tigr/ tigrfam
Module neighborhood information for RSP_2907

RSP_2907 has total of 29 gene neighbors in modules 156, 178
Gene neighbors (29)
Gene Common Name Description Module membership
RSP_0171 RSP_0171 Response regulator receiver protein (NCBI) 178, 291
RSP_0183 dht phenylhydantoinase (RefSeq) 156, 190
RSP_0236 RSP_0236 AgaE protein (NCBI) 156, 248
RSP_1046 RSP_1046 hypothetical protein (NCBI) 156, 190
RSP_1125 MltB Membrane bound lytic murein transglycosylase B (NCBI) 156, 190
RSP_1227 parA putative chromosome partitioning protein, ParA (NCBI) 178, 182
RSP_1552 RSP_1552 putative ureidoglycolate hydrolase (NCBI) 156, 190
RSP_1687 hbdA S(+)-beta-hydroxybutyryl CoA dehydrogenase (NCBI) 174, 178
RSP_1697 RSP_1697 hypothetical protein (NCBI) 156, 190
RSP_1841 RSP_1841 Probable intracellular septation protein (NCBI) 156, 190
RSP_1842 RSP_1842 possible transporter, DME family, DMT superfamily (NCBI) 156, 190
RSP_2135 RSP_2135 hypothetical protein (NCBI) 124, 156
RSP_2137 RSP_2137 hypothetical protein (NCBI) 156, 190
RSP_2138 fumC Fumarate lyase (NCBI) 156, 190
RSP_2266 rluB Pseudouridine synthase, (predicted) (NCBI) 156, 248
RSP_2293 clpA Chaperonin clpA/B (NCBI) 178, 289
RSP_2683 RSP_2683 hypothetical protein (NCBI) 178, 365
RSP_2685 RSP_2685 Putative cytochrome c-type biogenesis protein, cycH (NCBI) 178, 365
RSP_2686 RSP_2686 putative sarcosine oxidase beta subunit (NCBI) 178, 365
RSP_2723 RSP_2723 Isopropylmalate/homocitrate/citramalate synthases (NCBI) 156, 159
RSP_2724 RSP_2724 Probable Methylase involved in ubiquinone/menaquinone biosynthesis (NCBI) 156, 159
RSP_2725 RSP_2725 Probable Phytoene/squalene synthetase (NCBI) 156, 159
RSP_2816 RSP_2816 hypothetical protein (NCBI) 63, 178
RSP_2907 prfA peptide chain release factor 1 (NCBI) 156, 178
RSP_3010 RSP_3010 None 99, 178
RSP_3113 dadA D-amino acid dehydrogenase small subunit (NCBI) 178, 280
RSP_3596 lnt Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (NCBI) 156, 190
RSP_6011 RSP_6011 Putative transposase protein (NCBI) 33, 156
RSP_6030 RSP_6030 hypothetical protein (NCBI) 156, 194
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_2907
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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