Organism : Geobacter sulfurreducens | Module List :
GSU3045 flgM

negative regulator of flagellin synthesis FlgM (NCBI)

CircVis
Functional Annotations (5)
Function System
transcription repressor activity go/ molecular_function
flagellum go/ cellular_component
negative regulation of transcription, DNA-dependent go/ biological_process
Flagellar assembly kegg/ kegg pathway
FlgM_jcvi tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3045
(Mouseover regulator name to see its description)

GSU3045 is regulated by 23 influences and regulates 24 modules.
Regulators for GSU3045 flgM (23)
Regulator Module Operator
GSU0041 41 tf
GSU0178 41 tf
GSU0187 41 tf
GSU0682 41 tf
GSU1320 41 tf
GSU1617 41 tf
GSU2753 41 tf
GSU2817 41 tf
GSU2964 41 tf
GSU3041 41 tf
GSU3045 41 tf
GSU3089 41 tf
GSU3109 41 tf
GSU0031 185 tf
GSU0041 185 tf
GSU0178 185 tf
GSU0732 185 tf
GSU2149 185 tf
GSU2817 185 tf
GSU3041 185 tf
GSU3045 185 tf
GSU3053 185 tf
GSU3324 185 tf

Warning: GSU3045 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
2242 9.60e+02 GTtTgAACagAAA
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2243 7.50e+03 gggAacgtGCCgtTt
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2530 1.20e+03 aagaaaAAAAG
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2531 1.30e+03 cGgAcGaA
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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 GSU3045

GSU3045 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
transcription repressor activity go/ molecular_function
flagellum go/ cellular_component
negative regulation of transcription, DNA-dependent go/ biological_process
Flagellar assembly kegg/ kegg pathway
FlgM_jcvi tigr/ tigrfam
Module neighborhood information for GSU3045

GSU3045 has total of 30 gene neighbors in modules 41, 185
Gene neighbors (30)
Gene Common Name Description Module membership
GSU0041 lexA-1 LexA repressor (NCBI) 185, 242
GSU0042 GSU0042 hypothetical protein (VIMSS) 41, 185
GSU0043 dinP ImpB/MucB/SamB family protein (NCBI) 185, 242
GSU0052 GSU0052 hypothetical protein (VIMSS) 41, 246
GSU0053 GSU0053 hypothetical protein (VIMSS) 41, 317
GSU0054 GSU0054 hypothetical protein (VIMSS) 41, 242
GSU0169 GSU0169 ABC transporter, ATP-binding protein (VIMSS) 185, 242
GSU0407 flgB flagellar basal-body rod protein FlgB (NCBI) 185, 242
GSU0409 fliE flagellar hook-basal body complex protein FliE (NCBI) 41, 234
GSU0415 GSU0415 hypothetical protein (VIMSS) 185, 242
GSU0420 GSU0420 flagellar protein FliL (VIMSS) 185, 242
GSU0469 GSU0469 hypothetical protein (VIMSS) 41, 187
GSU0587 thiE thiamine-phosphate pyrophosphorylase (NCBI) 41, 185
GSU1185 GSU1185 conserved hypothetical protein (VIMSS) 41, 157
GSU2626 GSU2626 conserved hypothetical protein (VIMSS) 41, 234
GSU2639 GSU2639 hypothetical protein (VIMSS) 41, 61
GSU2829 phrB deoxyribodipyrimidine photolyase, putative (NCBI) 185, 242
GSU2903 GSU2903 conserved domain protein (VIMSS) 41, 234
GSU2911 GSU2911 hypothetical protein (VIMSS) 185, 242
GSU3014 GSU3014 HD domain protein (NCBI) 185, 242
GSU3035 GSU3035 hypothetical protein (VIMSS) 185, 242
GSU3038 fliC flagellin FliC (NCBI) 41, 242
GSU3040 yviF conserved hypothetical protein (NCBI) 185, 271
GSU3041 csrA carbon storage regulator (NCBI) 185, 271
GSU3042 flgL flagellar hook-associated protein FlgL (NCBI) 185, 271
GSU3045 flgM negative regulator of flagellin synthesis FlgM (NCBI) 41, 185
GSU3222 GSU3222 NHL repeat domain protein (NCBI) 41, 242
GSU3249 GSU3249 hypothetical protein (VIMSS) 41, 61
GSU3414 GSU3414 hypothetical protein (VIMSS) 41, 157
GSU3437 GSU3437 sensory box histidine kinase (VIMSS) 41, 246
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 GSU3045
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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