Organism : Geobacter sulfurreducens | Module List :
GSU2365 rfbD

dTDP-4-dehydrorhamnose reductase (NCBI)

CircVis
Functional Annotations (8)
Function System
dTDP-4-dehydrorhamnose reductase cog/ cog
dTDP-4-dehydrorhamnose reductase activity go/ molecular_function
extracellular polysaccharide biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Polyketide sugar unit biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
rmlD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2365
(Mouseover regulator name to see its description)

GSU2365 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU2365 rfbD (19)
Regulator Module Operator
GSU0041 174 tf
GSU0187 174 tf
GSU1320 174 tf
GSU1495 174 tf
GSU1831 174 tf
GSU2809 174 tf
GSU2964 174 tf
GSU3041 174 tf
GSU3324 174 tf
GSU3370 174 tf
GSU0187 306 tf
GSU0682 306 tf
GSU1495 306 tf
GSU1525 306 tf
GSU1831 306 tf
GSU2506 306 tf
GSU3041 306 tf
GSU3045 306 tf
GSU3324 306 tf

Warning: GSU2365 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
2508 3.10e-07 aacacCTagaTTTACCTcatTtTC
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2509 5.30e-05 GgagcGCCagCcGcaaaAaGG
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2768 1.80e+03 AccgtGcgGaTCAGggggAGggga
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2769 6.80e+02 GTGAcgctTt.TtAtAAAAA
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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 GSU2365

GSU2365 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
dTDP-4-dehydrorhamnose reductase cog/ cog
dTDP-4-dehydrorhamnose reductase activity go/ molecular_function
extracellular polysaccharide biosynthetic process go/ biological_process
Streptomycin biosynthesis kegg/ kegg pathway
Polyketide sugar unit biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
rmlD tigr/ tigrfam
Module neighborhood information for GSU2365

GSU2365 has total of 34 gene neighbors in modules 174, 306
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0020 GSU0020 hexapeptide transferase family protein (VIMSS) 174, 332
GSU0285 radA DNA repair protein RadA (NCBI) 15, 174
GSU0456 GSU0456 membrane protein, putative (VIMSS) 174, 221
GSU0558 GSU0558 hypothetical protein (VIMSS) 16, 174
GSU0633 GSU0633 glycosyl transferase, group 2 family protein (VIMSS) 31, 306
GSU0859 galU UTP-glucose-1-phosphate uridylyltransferase (NCBI) 209, 306
GSU0870 mutT mutator mutT protein (NCBI) 106, 306
GSU0880 GSU0880 molybdopterin oxidoreductase family protein (NCBI) 174, 306
GSU0998 dnaB replicative DNA helicase (NCBI) 282, 306
GSU1076 ruvA Holliday junction DNA helicase RuvA (NCBI) 39, 174
GSU1210 GSU1210 metallo-beta-lactamase family protein (NCBI) 174, 196
GSU1320 GSU1320 sigma-54 dependent DNA-binding response regulator (VIMSS) 14, 174
GSU1434 GSU1434 peptide ABC transporter, permease protein (VIMSS) 68, 306
GSU1438 GSU1438 conserved hypothetical protein (VIMSS) 204, 306
GSU1755 pyrD dihydroorotate dehydrogenase (NCBI) 143, 174
GSU1756 GSU1756 dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) 174, 196
GSU1797 GSU1797 ComEA-related protein (VIMSS) 106, 306
GSU1802 GSU1802 YjeF family protein (VIMSS) 260, 306
GSU1813 GSU1813 hypothetical protein (VIMSS) 31, 306
GSU1815 GSU1815 NAD-dependent epimerase/dehydratase family protein (VIMSS) 31, 306
GSU1891 GSU1891 response regulator (VIMSS) 215, 306
GSU1893 GSU1893 carbohydrate isomerase, KpsF/GutQ family (VIMSS) 81, 306
GSU1896 kdsB 3-deoxy-D-manno-octulosonate cytidylyltransferase (NCBI) 31, 306
GSU1929 GSU1929 MgtC family protein (VIMSS) 174, 306
GSU1930 mglA1 GTP-binding domain protein (NCBI) 174, 332
GSU1933 fusA-1 translation elongation factor G (NCBI) 174, 196
GSU2138 GSU2138 hypothetical protein (VIMSS) 174, 318
GSU2169 GSU2169 hypothetical protein (VIMSS) 96, 174
GSU2236 relA GTP pyrophosphokinase (NCBI) 102, 306
GSU2365 rfbD dTDP-4-dehydrorhamnose reductase (NCBI) 174, 306
GSU2558 GSU2558 conserved domain protein (VIMSS) 39, 174
GSU2886 GSU2886 TonB-dependent receptor, putative (VIMSS) 254, 306
GSU2928 GSU2928 hypothetical protein (VIMSS) 174, 282
GSU3081 GSU3081 conserved hypothetical protein, truncation (NCBI) 174, 201
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 GSU2365
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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