Organism : Geobacter sulfurreducens | Module List :
GSU3054

ParA family protein (VIMSS)

CircVis
Functional Annotations (7)
Function System
ATPases involved in chromosome partitioning cog/ cog
ATP binding go/ molecular_function
electron transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
oxidoreductase activity go/ molecular_function
cobyrinic acid a,c-diamide synthase activity go/ molecular_function
Flagellar assembly kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3054
(Mouseover regulator name to see its description)

GSU3054 is regulated by 15 influences and regulates 0 modules.
Regulators for GSU3054 (15)
Regulator Module Operator
GSU1522 186 tf
GSU1626 186 tf
GSU2581 186 tf
GSU2666 186 tf
GSU2716 186 tf
GSU2915 186 tf
GSU3229 186 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: GSU3054 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
2532 3.30e+03 AaAtcTgtTaT
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2533 2.40e+03 gGaaaCGagCcaTcTtcgtCt
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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 GSU3054

GSU3054 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
ATPases involved in chromosome partitioning cog/ cog
ATP binding go/ molecular_function
electron transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
oxidoreductase activity go/ molecular_function
cobyrinic acid a,c-diamide synthase activity go/ molecular_function
Flagellar assembly kegg/ kegg pathway
Module neighborhood information for GSU3054

GSU3054 has total of 36 gene neighbors in modules 186, 312
Gene neighbors (36)
Gene Common Name Description Module membership
GSU0093 GSU0093 ABC transporter, ATP-binding/permease protein (VIMSS) 86, 186
GSU0166 GSU0166 hypothetical protein (VIMSS) 312, 336
GSU0265 GSU0265 membrane protein, putative (VIMSS) 21, 186
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
GSU0411 fliG flagellar motor switch protein FliG (NCBI) 14, 186
GSU0412 GSU0412 flagellar assembly protein fliH, putative (VIMSS) 186, 322
GSU0413 fliI flagellum-specific ATP synthase FliI (NCBI) 186, 278
GSU0423 fliP flagellar biosynthetic protein FliP (NCBI) 109, 186
GSU0574 GSU0574 membrane protein, putative (VIMSS) 96, 186
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
GSU0738 GSU0738 hypothetical protein (VIMSS) 97, 186
GSU0916 GSU0916 methyl-accepting chemotaxis protein (VIMSS) 186, 287
GSU1098 pstC phosphate ABC transporter, permease protein (NCBI) 246, 312
GSU1140 GSU1140 methyl-accepting chemotaxis protein (VIMSS) 186, 241
GSU1141 GSU1141 methyl-accepting chemotaxis protein (VIMSS) 186, 241
GSU1143 cheR-2 chemotaxis protein methyltransferase CheR (NCBI) 186, 241
GSU2581 GSU2581 sigma-54 dependent transcriptional regulator (VIMSS) 14, 186
GSU2901 GSU2901 membrane protein, putative (VIMSS) 186, 266
GSU2904 GSU2904 hypothetical protein (NCBI) 186, 257
GSU2942 GSU2942 methyl-accepting chemotaxis protein (VIMSS) 186, 224
GSU2985 znuB ATPase component of zinc ABC transporter (Dmitry Rodionov) 109, 186
GSU3046 flgJ flagellar protein FlgJ-like protein (NCBI) 271, 312
GSU3047 flgI flagellar P-ring protein FlgI (NCBI) 141, 186
GSU3048 flgH flagellar L-ring protein FlgH (NCBI) 95, 186
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 GSU3054
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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