Organism : Geobacter sulfurreducens | Module List :
GSU0659

polysaccharide deacetylase domain protein (VIMSS)

CircVis
Functional Annotations (3)
Function System
Predicted xylanase/chitin deacetylase cog/ cog
carbohydrate metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0659
(Mouseover regulator name to see its description)

GSU0659 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0659 (17)
Regulator Module Operator
GSU1320 14 tf
GSU1626 14 tf
GSU2581 14 tf
GSU2587 14 tf
GSU2716 14 tf
GSU2753 14 tf
GSU3217 14 tf
GSU0280 97 tf
GSU0721 97 tf
GSU1013 97 tf
GSU1586 97 tf
GSU1934 97 tf
GSU2113 97 tf
GSU2506 97 tf
GSU2670 97 tf
GSU2753 97 tf
GSU2787 97 tf

Warning: GSU0659 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
2188 9.80e+03 TattaTtataaTgtaTACatT
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2189 4.30e+02 GcGgTgcTcctGGTG.TgGcG
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2354 1.90e+04 ttaCtgaacAAacaGaaTaaaca
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2355 5.20e+04 AATTaGTTTcaGTTA
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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 GSU0659

GSU0659 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted xylanase/chitin deacetylase cog/ cog
carbohydrate metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
Module neighborhood information for GSU0659

GSU0659 has total of 45 gene neighbors in modules 14, 97
Gene neighbors (45)
Gene Common Name Description Module membership
GSU0121 GSU0121 nickel-iron hydrogenase, b-type cytochrome subunit (VIMSS) 14, 266
GSU0260 GSU0260 universal stress protein family (VIMSS) 14, 178
GSU0311 GSU0311 hypothetical protein (VIMSS) 78, 97
GSU0394 GSU0394 AcrB/AcrD/AcrF family protein (VIMSS) 14, 229
GSU0411 fliG flagellar motor switch protein FliG (NCBI) 14, 186
GSU0571 folA dihydrofolate reductase (NCBI) 14, 281
GSU0659 GSU0659 polysaccharide deacetylase domain protein (VIMSS) 14, 97
GSU0738 GSU0738 hypothetical protein (VIMSS) 97, 186
GSU0844 GSU0844 potassium uptake protein, Trk family (VIMSS) 46, 97
GSU0846 acnA aconitate hydratase 1 (NCBI) 97, 160
GSU1031 GSU1031 hypothetical protein (VIMSS) 14, 337
GSU1046 GSU1046 conserved hypothetical protein (VIMSS) 97, 127
GSU1064 GSU1064 hypothetical protein (VIMSS) 14, 220
GSU1154 GSU1154 surface repeat protein, putative (NCBI) 14, 268
GSU1204 GSU1204 sodium/hydrogen exchanger family/TrkA domain protein (VIMSS) 14, 282
GSU1300 GSU1300 methyl-accepting chemotaxis protein (VIMSS) 14, 78
GSU1320 GSU1320 sigma-54 dependent DNA-binding response regulator (VIMSS) 14, 174
GSU1371 GSU1371 oxidoreductase, FAD/FMN-binding (NCBI) 14, 107
GSU1482 GSU1482 outer membrane efflux protein (VIMSS) 14, 295
GSU1563 GSU1563 hypothetical protein (VIMSS) 97, 164
GSU1769 GSU1769 conserved hypothetical protein (VIMSS) 97, 113
GSU1856 GSU1856 None 97, 151
GSU1948 GSU1948 hypothetical protein (VIMSS) 14, 292
GSU2142 GSU2142 hypothetical protein (VIMSS) 97, 311
GSU2347 GSU2347 conserved hypothetical protein (VIMSS) 97, 190
GSU2348 GSU2348 conserved hypothetical protein (VIMSS) 49, 97
GSU2403 GSU2403 hypothetical protein (VIMSS) 65, 97
GSU2404 GSU2404 pentapeptide repeat domain protein (VIMSS) 97, 325
GSU2482 kdpC potassium-transporting ATPase, C subunit (NCBI) 49, 97
GSU2506 GSU2506 sensory box protein/sigma-54 dependent DNA-binding response regulator (NCBI) 97, 341
GSU2581 GSU2581 sigma-54 dependent transcriptional regulator (VIMSS) 14, 186
GSU2752 GSU2752 hypothetical protein (VIMSS) 90, 97
GSU2815 GSU2815 sensory box histidine kinase (VIMSS) 97, 317
GSU2884 GSU2884 cytochrome c family protein (VIMSS) 2, 97
GSU2885 GSU2885 NHL repeat domain protein (VIMSS) 2, 97
GSU2907 GSU2907 membrane protein, putative (VIMSS) 14, 109
GSU2959 GSU2959 membrane protein, putative (NCBI) 14, 213
GSU2981 GSU2981 TonB-dependent receptor, putative (VIMSS) 14, 148
GSU3011 GSU3011 hypothetical protein (VIMSS) 97, 101
GSU3039 GSU3039 hypothetical protein (VIMSS) 97, 140
GSU3073 GSU3073 None 52, 97
GSU3319 ppiA peptidyl-prolyl cis-trans isomerase A (NCBI) 97, 317
GSU3409 GSU3409 hypothetical protein (VIMSS) 97, 206
GSU3410 GSU3410 hypothetical protein (VIMSS) 97, 206
GSU3419 GSU3419 sensor histidine kinase (VIMSS) 14, 274
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 GSU0659
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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