Organism : Geobacter sulfurreducens | Module List :
GSU3387

transcriptional regulator, AraC/XylS family (VIMSS)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3387
(Mouseover regulator name to see its description)

GSU3387 is regulated by 19 influences and regulates 43 modules.
Regulators for GSU3387 (19)
Regulator Module Operator
GSU0266 283 tf
GSU0366 283 tf
GSU0473 283 tf
GSU1115 283 tf
GSU1268 283 tf
GSU1617 283 tf
GSU3217 283 tf
GSU3229 283 tf
GSU3387 283 tf
GSU3396 283 tf
GSU0266 92 tf
GSU0770 92 tf
GSU1626 92 tf
GSU1989 92 tf
GSU2524 92 tf
GSU2915 92 tf
GSU3108 92 tf
GSU3217 92 tf
GSU3387 92 tf

Warning: GSU3387 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
2344 2.10e+03 gTgtTAaCG.Aagcg.aAa...G
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2345 2.10e+04 GGcaTCaCcGCTgTC
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2726 1.30e+02 cAtGAAAA
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2727 2.40e+03 ctgcTattAT.GacCgGaA
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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 GSU3387

GSU3387 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for GSU3387

GSU3387 has total of 34 gene neighbors in modules 92, 283
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0046 GSU0046 ISGsu6, transposase OrfA (VIMSS) 92, 211
GSU0238 GSU0238 radical SAM domain protein (NCBI) 119, 283
GSU0252 GSU0252 ISGsu1, transposase (VIMSS) 92, 211
GSU0286 GSU0286 PBS lyase HEAT-like repeat protein (NCBI) 92, 107
GSU0374 hypA hydrogenase expression/formation protein hupa (NCBI) 283, 304
GSU0386 radC DNA repair protein RadC (NCBI) 89, 283
GSU0398 GSU0398 phage shock protein E, putative (VIMSS) 92, 163
GSU0410 fliF flagellar M-ring protein FliF (NCBI) 132, 283
GSU0424 fliQ flagellar biosynthetic protein FliQ (NCBI) 92, 217
GSU0699 GSU0699 HD domain protein (NCBI) 148, 283
GSU0704 GSU0704 hypothetical protein (VIMSS) 283, 291
GSU0828 GSU0828 metal ion efflux outer membrane protein family protein, putative (VIMSS) 27, 92
GSU0922 GSU0922 ABC transporter, ATP-binding protein (VIMSS) 20, 283
GSU0949 GSU0949 efflux transporter, RND family, MFP subunit (NCBI) 144, 283
GSU0955 GSU0955 group II intron, maturase (VIMSS) 92, 211
GSU0961 GSU0961 ISGsu4, transposase (VIMSS) 92, 211
GSU0993 GSU0993 conserved hypothetical protein (VIMSS) 283, 293
GSU1012 GSU1012 membrane protein, putative (VIMSS) 213, 283
GSU1020 GSU1020 hypothetical protein (VIMSS) 92, 132
GSU1400 GSU1400 None 38, 92
GSU1767 xseA exodeoxyribonuclease VII, large subunit (NCBI) 92, 218
GSU2320 GSU2320 hypothetical protein (VIMSS) 92, 294
GSU2343 GSU2343 None 92, 132
GSU2346 GSU2346 membrane protein, putative (VIMSS) 92, 107
GSU2373 GSU2373 lipoprotein, putative (VIMSS) 63, 283
GSU2422 GSU2422 hydrogenase maturation protease (VIMSS) 283, 293
GSU2500 GSU2500 hypothetical protein (NCBI) 92, 213
GSU2532 GSU2532 conserved hypothetical protein (VIMSS) 180, 283
GSU2766 GSU2766 decarboxylase family protein (NCBI) 132, 283
GSU3217 GSU3217 sigma-54 dependent DNA-binding response regulator (VIMSS) 92, 287
GSU3232 GSU3232 cytochrome c family protein, putative (NCBI) 283, 337
GSU3315 GSU3315 major facilitator family transporter (VIMSS) 132, 283
GSU3387 GSU3387 transcriptional regulator, AraC/XylS family (VIMSS) 92, 283
GSU3431 nuoL-2 NADH dehydrogenase I, L subunit (NCBI) 283, 336
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 GSU3387
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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