Organism : Geobacter sulfurreducens | Module List :
GSU1003 ntrC

nitrogen regulation protein NR(I) (NCBI)

CircVis
Functional Annotations (10)
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
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1003
(Mouseover regulator name to see its description)

GSU1003 is regulated by 13 influences and regulates 12 modules.
Regulators for GSU1003 ntrC (13)
Regulator Module Operator
GSU0655 89 tf
GSU1003 89 tf
GSU1617 89 tf
GSU2177 89 tf
GSU2698 89 tf
GSU3087 89 tf
GSU3298 89 tf
GSU3396 89 tf
GSU0013 265 tf
GSU0300 265 tf
GSU0736 265 tf
GSU1013 265 tf
GSU2868 265 tf

Warning: GSU1003 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
2338 2.30e-02 C.aTGAAA.aaattACAaCAg
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2339 1.10e-01 aAAAcGCaAtCtTTgttTt
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2690 9.60e-05 AAAaAtagtAcCtTaTAtTtTt.T
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2691 1.50e-02 GTCAATaAc.TcaaAgGacg
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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 GSU1003

GSU1003 is enriched for 10 functions in 3 categories.
Module neighborhood information for GSU1003

GSU1003 has total of 47 gene neighbors in modules 89, 265
Gene neighbors (47)
Gene Common Name Description Module membership
GSU0015 GSU0015 PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0016 ppiD PPIC-type PPIASE domain protein (NCBI) 4, 89
GSU0018 GSU0018 transcriptional regulator, GntR family/aminotransferase class-I (VIMSS) 4, 89
GSU0019 GSU0019 pentapeptide repeat domain protein (VIMSS) 4, 89
GSU0386 radC DNA repair protein RadC (NCBI) 89, 283
GSU0387 GSU0387 undecaprenol kinase, putative (VIMSS) 89, 295
GSU0388 GSU0388 conserved hypothetical protein (NCBI) 89, 264
GSU0389 GSU0389 phosphate transporter, putative (VIMSS) 26, 89
GSU0443 GSU0443 ribonuclease D, putative (VIMSS) 89, 295
GSU0487 GSU0487 cation efflux family protein (VIMSS) 144, 265
GSU0529 nfo endonuclease IV (NCBI) 89, 225
GSU0734 GSU0734 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0736 GSU0736 pemK protein, putative (VIMSS) 238, 265
GSU0737 GSU0737 hypothetical protein (NCBI) 265, 276
GSU0739 GSU0739 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0740 GSU0740 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0741 GSU0741 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0742 GSU0742 NAD-dependent dehydrogenase subunit (VIMSS) 222, 265
GSU0743 GSU0743 NAD-dependent dehydrogenase subunit (VIMSS) 158, 265
GSU0744 GSU0744 hypothetical protein (VIMSS) 238, 265
GSU0876 GSU0876 diacylglycerol kinase catalytic domain protein (NCBI) 89, 322
GSU1002 GSU1002 isochorismatase family protein (NCBI) 89, 265
GSU1003 ntrC nitrogen regulation protein NR(I) (NCBI) 89, 265
GSU1004 GSU1004 sensory box histidine kinase (VIMSS) 89, 265
GSU1006 GSU1006 hypothetical protein (VIMSS) 265, 335
GSU1136 GSU1136 5-formyltetrahydrofolate cyclo-ligase family protein (VIMSS) 249, 265
GSU1741 GSU1741 phosphatase, Ppx/GppA family (VIMSS) 68, 265
GSU1745 GSU1745 OmpA domain protein (VIMSS) 236, 265
GSU1746 ihfB integration host factor, beta subunit (NCBI) 11, 265
GSU1881 ptsI phosphoenolpyruvate-protein phosphotransferase (NCBI) 245, 265
GSU2551 GSU2551 LysM domain protein (VIMSS) 89, 231
GSU2619 tgt-2 queuine tRNA-ribosyltransferase (NCBI) 89, 231
GSU2989 GSU2989 L-threonine-O-3-phosphate decarboxylase, putative (VIMSS) 89, 281
GSU2991 GSU2991 sensor histidine kinase (VIMSS) 89, 285
GSU2992 cobQ cobyric acid synthase (NCBI) 89, 153
GSU2997 cbiD cobalamin biosynthesis protein CbiD (NCBI) 89, 281
GSU2998 GSU2998 nitroimidazole resistance protein, putative (VIMSS) 89, 169
GSU2999 cobH precorrin-8X methylmutase (VIMSS) 265, 285
GSU3000 GSU3000 cbiX protein (NCBI) 183, 265
GSU3002 GSU3002 cobalt ABC transporter, permease protein (VIMSS) 89, 285
GSU3004 GSU3004 cobalt transport protein CbiM (RefSeq) 75, 89
GSU3010 cobU bifunctional cobalamin biosynthesis protein CobU (NCBI) 30, 89
GSU3064 ftsA cell division protein FtsA (NCBI) 249, 265
GSU3283 GSU3283 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 44, 89
GSU3286 hemD uroporphyrinogen III synthase/methyltransferase (NCBI) 89, 300
GSU3287 GSU3287 hydrolase, TatD family (NCBI) 30, 89
GSU3288 moeB thiF family protein (NCBI) 30, 89
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 GSU1003
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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