Organism : Geobacter sulfurreducens | Module List :
GSU1095 phoU

phosphate transport system regulatory protein PhoU (NCBI)

CircVis
Functional Annotations (2)
Function System
Phosphate uptake regulator cog/ cog
phoU_full tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1095
(Mouseover regulator name to see its description)

GSU1095 is regulated by 15 influences and regulates 11 modules.
Regulators for GSU1095 phoU (15)
Regulator Module Operator
GSU0164 1 tf
GSU1095 1 tf
GSU2587 1 tf
GSU2868 1 tf
GSU2915 1 tf
GSU3217 1 tf
GSU0473 96 tf
GSU0896 96 tf
GSU1095 96 tf
GSU1129 96 tf
GSU1626 96 tf
GSU2581 96 tf
GSU2716 96 tf
GSU2915 96 tf
GSU3363 96 tf

Warning: GSU1095 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
2162 2.20e+00 aaacggaCAagGaGa
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2163 8.60e+03 caCCACAaCcCtacgGgGga
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2352 6.00e+01 TaAcGTgTTATcaTt
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2353 3.20e+02 tTattA.gTgaaaAtgA
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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 GSU1095

GSU1095 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Phosphate uptake regulator cog/ cog
phoU_full tigr/ tigrfam
Module neighborhood information for GSU1095

GSU1095 has total of 47 gene neighbors in modules 1, 96
Gene neighbors (47)
Gene Common Name Description Module membership
GSU0123 GSU0123 nickel-dependent hydrogenase, small subunit (VIMSS) 96, 252
GSU0356 GSU0356 None 96, 107
GSU0373 GSU0373 sensor histidine kinase (VIMSS) 96, 220
GSU0396 GSU0396 conserved hypothetical protein (VIMSS) 96, 229
GSU0427 GSU0427 lipoprotein, putative (VIMSS) 96, 278
GSU0431 GSU0431 conserved hypothetical protein (VIMSS) 96, 130
GSU0432 GSU0432 conserved hypothetical protein (VIMSS) 96, 278
GSU0433 GSU0433 clpB protein, putative (NCBI) 21, 96
GSU0449 GSU0449 hypothetical protein (VIMSS) 96, 137
GSU0574 GSU0574 membrane protein, putative (VIMSS) 96, 186
GSU0801 GSU0801 hypothetical protein (VIMSS) 96, 109
GSU1032 GSU1032 methyl-accepting chemotaxis protein (VIMSS) 1, 337
GSU1037 GSU1037 sensory box/response regulator (VIMSS) 1, 224
GSU1095 phoU phosphate transport system regulatory protein PhoU (NCBI) 1, 96
GSU1146 GSU1146 conserved domain protein (NCBI) 96, 109
GSU1407 GSU1407 hypothetical protein (VIMSS) 1, 268
GSU1676 GSU1676 hypothetical protein (VIMSS) 96, 236
GSU1988 GSU1988 hypothetical protein (VIMSS) 96, 206
GSU2094 GSU2094 response regulator (VIMSS) 1, 287
GSU2095 GSU2095 NADH oxidase, putative (VIMSS) 1, 79
GSU2098 cooS carbon monoxide dehydrogenase subunit (NCBI) 1, 178
GSU2115 GSU2115 hypothetical protein (VIMSS) 1, 16
GSU2152 GSU2152 hypothetical protein (VIMSS) 1, 213
GSU2154 GSU2154 hypothetical protein (VIMSS) 1, 337
GSU2156 GSU2156 hypothetical protein (VIMSS) 1, 70
GSU2158 norQ cobS protein, putative (NCBI) 1, 322
GSU2162 GSU2162 hypothetical protein (VIMSS) 1, 224
GSU2165 GSU2165 hypothetical protein (VIMSS) 1, 78
GSU2166 GSU2166 hypothetical protein (VIMSS) 1, 300
GSU2167 GSU2167 CHC2 zinc finger domain protein (VIMSS) 1, 78
GSU2168 radC DNA repair protein RadC (NCBI) 1, 163
GSU2169 GSU2169 hypothetical protein (VIMSS) 96, 174
GSU2309 GSU2309 metallo-beta-lactamase family protein (VIMSS) 96, 130
GSU2372 GSU2372 methyl-accepting chemotaxis protein, putative (VIMSS) 96, 220
GSU2421 GSU2421 hypothetical protein (VIMSS) 1, 190
GSU2480 kdpA potassium-transporting ATPase, A subunit (NCBI) 96, 252
GSU2481 kdpB potassium-transporting ATPase, B subunit (NCBI) 96, 257
GSU2484 kdpE DNA-binding response regulator KdpE (NCBI) 96, 257
GSU2534 GSU2534 sensory box/response regulator (VIMSS) 96, 266
GSU2661 GSU2661 conserved hypothetical protein (VIMSS) 1, 287
GSU2776 GSU2776 conserved hypothetical protein (NCBI) 1, 9
GSU2984 znuC permease component of zinc ABC transporter (Dmitry Rodionov) 96, 287
GSU3019 GSU3019 dehydrogenase, E1 component, alpha and beta subunits (NCBI) 27, 96
GSU3121 GSU3121 EF hand domain protein (VIMSS) 1, 224
GSU3180 GSU3180 conserved hypothetical protein (VIMSS) 1, 180
GSU3239 cafA ribonuclease G (NCBI) 96, 236
GSU3400 GSU3400 heavy metal efflux pump, CzcA family (VIMSS) 1, 337
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 GSU1095
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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