Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0405

probable single-stranded DNA-specific exonuclease (NCBI)

CircVis
Functional Annotations (10)
Function System
Single-stranded DNA-specific exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
5'-3' exonuclease activity go/ molecular_function
manganese ion binding go/ molecular_function
Base excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
recJ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0405
(Mouseover regulator name to see its description)

RSP_0405 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_0405 (20)
Regulator Module Operator
RSP_0090 110 tf
RSP_0507 110 tf
RSP_0623 110 tf
RSP_0755 110 tf
RSP_0907 110 tf
RSP_2236 110 tf
RSP_2346 110 tf
RSP_2533 110 tf
RSP_2838 110 tf
RSP_2840 110 tf
RSP_3606 110 tf
RSP_0032 20 tf
RSP_0090 20 tf
RSP_1550 20 tf
RSP_1590 20 tf
RSP_1871 20 tf
RSP_1936 20 tf
RSP_2610 20 tf
RSP_2840 20 tf
RSP_3203 20 tf

Warning: RSP_0405 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
7760 1.50e+02 GaTgaAac
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7761 7.40e+03 AGGAA.GTGA
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7940 3.50e+02 CAGCTTcTA.ttgtttTtctT
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7941 9.80e+03 TTC.GcgAGG
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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_0405

RSP_0405 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Single-stranded DNA-specific exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
5'-3' exonuclease activity go/ molecular_function
manganese ion binding go/ molecular_function
Base excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
recJ tigr/ tigrfam
Module neighborhood information for RSP_0405

RSP_0405 has total of 38 gene neighbors in modules 20, 110
Gene neighbors (38)
Gene Common Name Description Module membership
RSP_0089 RSP_0089 hypothetical protein (NCBI) 23, 110
RSP_0377 RSP_0377 probable glutamine synthetase (NCBI) 110, 259
RSP_0378 RSP_0378 hypothetical protein (NCBI) 110, 259
RSP_0405 RSP_0405 probable single-stranded DNA-specific exonuclease (NCBI) 20, 110
RSP_0449 RSP_0449 putative glutamine amidotransferase (NCBI) 20, 293
RSP_0667 RSP_0667 hypothetical protein (NCBI) 20, 326
RSP_0668 RSP_0668 OmpA/MotB family protein (NCBI) 20, 262
RSP_0897 RSP_0897 Glutathione S-transferase (NCBI) 10, 20
RSP_0898 DCOHM pterin dehydratase (NCBI) 20, 357
RSP_0907 dctR two component transcriptional regulator, LuxR family (NCBI) 110, 357
RSP_1030 RSP_1030 putative pfkB family carbohydrate kinase (NCBI) 110, 318
RSP_1031 RSP_1031 Endonuclease III (NCBI) 110, 384
RSP_1062 RSP_1062 ATPases of the PP superfamily (NCBI) 110, 209
RSP_1182 RSP_1182 putative outer membrane protein (NCBI) 110, 259
RSP_1183 RSP_1183 hypothetical protein (NCBI) 110, 259
RSP_1358 RSP_1358 hypothetical protein (NCBI) 110, 339
RSP_1359 recQ DEAD/DEAH box helicase (NCBI) 110, 339
RSP_1447 RSP_1447 possible glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI) 89, 110
RSP_1524 RSP_1524 Nucleotidyltransferase family protein (NCBI) 110, 176
RSP_1527 RSP_1527 Helicase, UvrD/Rep family (NCBI) 110, 157
RSP_1771 RSP_1771 beta subunit of citrate lyase (NCBI) 20, 112
RSP_1912 RSP_1912 hypothetical protein (NCBI) 110, 363
RSP_1976 cobT aerobic cobalt chelatase, CobT subunit (NCBI) 20, 256
RSP_2030 RSP_2030 putative sensor histidine kinase (NCBI) 20, 110
RSP_2102 RSP_2102 hypothetical protein (NCBI) 110, 146
RSP_2160 gno Short-chain dehydrogenase/reductase (NCBI) 20, 176
RSP_2207 deoD purine nucleoside phosphorylase (NCBI) 67, 110
RSP_2285 RSP_2285 conservd hypothetical protein (NCBI) 20, 339
RSP_2411 RSP_2411 hypothetical protein (NCBI) 20, 107
RSP_2476 RSP_2476 hypothetical protein (NCBI) 29, 110
RSP_2651 RSP_2651 hypothetical protein (NCBI) 7, 110
RSP_2652 RSP_2652 putative Acetyltransferase (NCBI) 7, 110
RSP_2908 RSP_2908 hypothetical protein (NCBI) 110, 384
RSP_2909 RSP_2909 Hydrolase arginase family (NCBI) 110, 384
RSP_3077 RSP_3077 hypothetical protein (NCBI) 110, 322
RSP_3151 RSP_3151 ABC nitrate/sulfonate/bicarbonate transporter family, periplasmic substrate-binding protein (NCBI) 105, 110
RSP_3153 RSP_3153 ABC nitrate/sulfonate/bicarbonate transporter family, inner membrane subunit (NCBI) 110, 251
RSP_3216 RSP_3216 putative DNA repair exonuclease (NCBI) 20, 67
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_0405
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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