Organism : Geobacter sulfurreducens | Module List :
GSU0963 ntrC

sigma-54 dependent DNA-binding response regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0963
(Mouseover regulator name to see its description)

GSU0963 is regulated by 15 influences and regulates 7 modules.
Regulators for GSU0963 ntrC (15)
Regulator Module Operator
GSU0018 32 tf
GSU0551 32 tf
GSU0963 32 tf
GSU1072 32 tf
GSU1483 32 tf
GSU1940 32 tf
GSU2185 32 tf
GSU3108 32 tf
GSU0018 142 tf
GSU0598 142 tf
GSU0963 142 tf
GSU1072 142 tf
GSU2779 142 tf
GSU2945 142 tf
GSU3109 142 tf

Warning: GSU0963 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
2224 1.20e+00 AATgctATtGcTataATgCAAa
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2225 1.40e+01 AagAAAGGAGTaACt
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2444 2.30e+00 TaAAATAAAaaaatAatTc
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2445 9.50e+02 TT.ccggaaaAcTtcaaaaAt.a
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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 GSU0963

GSU0963 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU0963

GSU0963 has total of 46 gene neighbors in modules 32, 142
Gene neighbors (46)
Gene Common Name Description Module membership
GSU0096 recR recombination protein RecR (NCBI) 32, 142
GSU0174 GSU0174 acetyl-CoA hydrolase/transferase family protein (VIMSS) 32, 308
GSU0175 GSU0175 transcriptional regulator, TetR family (VIMSS) 32, 308
GSU0229 alkK medium-chain-fatty-acid--CoA ligase (NCBI) 32, 93
GSU0261 GSU0261 sodium/hydrogen exchanger family protein (VIMSS) 32, 178
GSU0362 GSU0362 hypothetical protein (VIMSS) 142, 183
GSU0540 GSU0540 hypothetical protein (NCBI) 142, 156
GSU0851 GSU0851 rhomboid family protein (VIMSS) 32, 238
GSU0946 GSU0946 sensory box/GGDEF family protein (VIMSS) 32, 93
GSU0963 ntrC sigma-54 dependent DNA-binding response regulator (NCBI) 32, 142
GSU0966 GSU0966 hypothetical protein (VIMSS) 32, 93
GSU0967 GSU0967 membrane protein, putative (VIMSS) 32, 252
GSU1019 GSU1019 xanthine/uracil permease family protein (VIMSS) 32, 281
GSU1021 GSU1021 hypothetical protein (VIMSS) 93, 142
GSU1068 GSU1068 sodium/solute symporter family protein (NCBI) 32, 142
GSU1069 GSU1069 conserved hypothetical protein (VIMSS) 32, 142
GSU1070 GSU1070 sodium/solute symporter family protein (NCBI) 32, 142
GSU1071 GSU1071 conserved hypothetical protein (VIMSS) 32, 142
GSU1289 cheY-3 chemotaxis protein CheY (NCBI) 32, 146
GSU1305 gdhA Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 32, 122
GSU1325 GSU1325 hypothetical protein (NCBI) 99, 142
GSU1575 GSU1575 hypothetical protein (VIMSS) 32, 308
GSU1762 GSU1762 TPR domain protein (VIMSS) 32, 201
GSU2005 GSU2005 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) 135, 142
GSU2006 GSU2006 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2007 GSU2007 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2008 GSU2008 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 135, 142
GSU2009 GSU2009 branched-chain amino acid ABC transporter, ATP-binding protein (VIMSS) 135, 142
GSU2010 GSU2010 CBS domain protein (VIMSS) 135, 142
GSU2092 GSU2092 conserved hypothetical protein (VIMSS) 142, 295
GSU2103 GSU2103 hypothetical protein (VIMSS) 142, 281
GSU2150 GSU2150 hypothetical protein (VIMSS) 46, 142
GSU2352 GSU2352 sodium/solute symporter family protein (NCBI) 32, 122
GSU2353 GSU2353 conserved hypothetical protein (VIMSS) 32, 70
GSU2357 GSU2357 conserved hypothetical protein (VIMSS) 32, 142
GSU2358 GSU2358 isoamylase family protein (VIMSS) 79, 142
GSU2361 GSU2361 alpha amylase family protein (VIMSS) 9, 142
GSU2363 GSU2363 chloride channel family protein, putative (VIMSS) 32, 281
GSU2462 metA homoserine O-acetyltransferase (NCBI) 32, 93
GSU2490 GSU2490 oxalate/formate antiporter, putative (VIMSS) 32, 142
GSU2706 GSU2706 phosphate acetyltransferase (VIMSS) 32, 142
GSU2881 GSU2881 hypothetical protein (VIMSS) 122, 142
GSU2944 GSU2944 (R)-2-hydroxyglutaryl-CoA dehydratase alpha-subunit, putative (VIMSS) 32, 93
GSU2945 GSU2945 (R)-2-hydroxyglutaryl-CoA dehydratase activator, putative (VIMSS) 32, 93
GSU2982 GSU2982 TonB dependent receptor, putative (VIMSS) 32, 93
GSU3234 GSU3234 hypothetical protein (VIMSS) 142, 337
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 GSU0963
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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