Organism : Geobacter sulfurreducens | Module List :
GSU3053 fliA

RNA polymerase sigma factor for flagellar operon (NCBI)

CircVis
Functional Annotations (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
phosphatidylserine decarboxylase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3053
(Mouseover regulator name to see its description)

GSU3053 is regulated by 14 influences and regulates 20 modules.
Regulators for GSU3053 fliA (14)
Regulator Module Operator
GSU1320 296 tf
GSU1639 296 tf
GSU2787 296 tf
GSU2809 296 tf
GSU2915 296 tf
GSU3053 296 tf
GSU1483 312 tf
GSU1626 312 tf
GSU2581 312 tf
GSU2817 312 tf
GSU3041 312 tf
GSU3045 312 tf
GSU3053 312 tf
GSU3229 312 tf

Warning: GSU3053 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
2750 3.10e+00 TAaaATCcTTaAcAAaC
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2751 9.60e-01 GgCaTCCcttcTgCGgcGgaC
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2780 2.10e+01 tAta.tctCacaA.CaGGgAgaAc
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2781 3.20e+02 CaTAaAAAAa
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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 GSU3053

GSU3053 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
phosphatidylserine decarboxylase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
Module neighborhood information for GSU3053

GSU3053 has total of 42 gene neighbors in modules 296, 312
Gene neighbors (42)
Gene Common Name Description Module membership
GSU0166 GSU0166 hypothetical protein (VIMSS) 312, 336
GSU0291 cheR CheR methyltransferase, SAM binding domain protein, putative (NCBI) 36, 296
GSU0375 gcvT glycine cleavage system T protein (NCBI) 296, 304
GSU0376 gcvH-1 glycine cleavage system H protein (NCBI) 153, 296
GSU0377 GSU0377 glycine cleavage system P protein, subunit 1 (VIMSS) 153, 296
GSU0378 GSU0378 glycine cleavage system P protein, subunit 2 (VIMSS) 153, 296
GSU0379 GSU0379 biotin/lipoate A/B protein ligase family protein (NCBI) 153, 296
GSU0380 lipA lipoic acid synthetase (NCBI) 153, 296
GSU0381 GSU0381 lipoprotein, putative (VIMSS) 274, 296
GSU0382 GSU0382 conserved hypothetical protein (VIMSS) 153, 296
GSU0405 GSU0405 response regulator (VIMSS) 251, 312
GSU0406 GSU0406 TPR domain protein (VIMSS) 165, 312
GSU0408 flgC flagellar basal-body rod protein FlgC (NCBI) 280, 312
GSU0676 GSU0676 lipoprotein, putative (VIMSS) 118, 312
GSU0677 GSU0677 ABC transporter, permease protein, putative (VIMSS) 246, 312
GSU0678 GSU0678 ABC transporter, ATP-binding protein (VIMSS) 259, 312
GSU0698 GSU0698 PBS lyase HEAT-like repeat protein (NCBI) 296, 304
GSU0920 GSU0920 hypothetical protein (NCBI) 82, 296
GSU0951 GSU0951 transcriptional regulator, TetR family (VIMSS) 82, 296
GSU1098 pstC phosphate ABC transporter, permease protein (NCBI) 246, 312
GSU1315 merA-1 mercuric reductase (NCBI) 296, 304
GSU1326 recG ATP-dependent DNA helicase RecG (NCBI) 296, 298
GSU2336 otsB trehalose-phosphatase (NCBI) 296, 300
GSU2466 GSU2466 hypothetical protein (VIMSS) 39, 296
GSU2573 GSU2573 hypothetical protein (VIMSS) 104, 296
GSU2577 GSU2577 hypothetical protein (VIMSS) 296, 304
GSU2673 GSU2673 hypothetical protein (VIMSS) 144, 296
GSU2676 GSU2676 membrane protein, putative (VIMSS) 152, 296
GSU2780 GSU2780 hypothetical protein (VIMSS) 165, 296
GSU2781 GSU2781 efflux transporter, RND family, MFP subunit (NCBI) 130, 296
GSU2782 GSU2782 AcrB/AcrD/AcrF family protein (VIMSS) 278, 296
GSU2783 GSU2783 HDIG domain protein (VIMSS) 147, 296
GSU2973 GSU2973 lipoprotein, putative (VIMSS) 59, 296
GSU3046 flgJ flagellar protein FlgJ-like protein (NCBI) 271, 312
GSU3052 flgG-2 flagellar basal-body rod protein FlgG (NCBI) 186, 312
GSU3053 fliA RNA polymerase sigma factor for flagellar operon (NCBI) 296, 312
GSU3054 GSU3054 ParA family protein (VIMSS) 186, 312
GSU3055 GSU3055 flagellar biosynthetic protein FlhF, putative (VIMSS) 186, 312
GSU3056 flhA flagellar biosynthetic protein FlhA (NCBI) 294, 312
GSU3223 GSU3223 cytochrome c family protein (NCBI) 109, 312
GSU3424 merA-2 mercuric reductase (NCBI) 259, 312
GSU3425 GSU3425 hypothetical protein (VIMSS) 261, 312
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 GSU3053
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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