Organism : Geobacter sulfurreducens | Module List :
GSU2915

sigma-54 dependent DNA-binding response regulator (VIMSS)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2915
(Mouseover regulator name to see its description)

GSU2915 is regulated by 17 influences and regulates 57 modules.
Regulators for GSU2915 (17)
Regulator Module Operator
GSU0254 11 tf
GSU0266 11 tf
GSU0372 11 tf
GSU1115 11 tf
GSU1727 11 tf
GSU2587 11 tf
GSU2915 11 tf
GSU3387 11 tf
GSU3421 11 tf
GSU0207 116 tf
GSU0284 116 tf
GSU0770 116 tf
GSU1569 116 tf
GSU1586 116 tf
GSU1905 116 tf
GSU2831 116 tf
GSU2915 116 tf
Regulated by GSU2915 (57)
Module Residual Genes
1 0.44 23
10 0.30 15
11 0.45 25
13 0.27 17
17 0.47 25
24 0.28 4
34 0.55 9
36 0.51 16
42 0.50 21
48 0.34 17
50 0.48 22
54 0.51 7
55 0.52 8
58 0.33 21
62 0.33 19
63 0.48 19
79 0.44 29
92 0.31 17
94 0.56 16
96 0.45 25
108 0.52 7
110 0.51 17
113 0.48 28
116 0.41 20
117 0.34 19
132 0.33 14
140 0.47 34
148 0.49 17
154 0.32 15
156 0.31 16
163 0.34 18
180 0.51 19
186 0.50 22
189 0.57 29
190 0.48 21
197 0.33 16
206 0.46 27
207 0.50 22
213 0.39 20
217 0.33 19
220 0.45 20
224 0.53 25
226 0.32 17
228 0.48 25
232 0.33 21
258 0.45 23
262 0.53 29
264 0.55 28
266 0.48 27
267 0.51 20
278 0.47 32
282 0.31 13
293 0.40 23
296 0.52 26
298 0.58 7
304 0.50 27
333 0.32 19
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2182 4.20e-02 gAaGgcCgctacCcg.CcGacgtt
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2183 2.20e+02 AAcaAtcAAAt
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2392 1.40e+02 ataAaatTGACtAAt
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2393 8.10e+02 AaAAGTAA
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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 GSU2915

GSU2915 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU2915

GSU2915 has total of 44 gene neighbors in modules 11, 116
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0037 serS seryl-tRNA synthetase (NCBI) 37, 116
GSU0207 GSU0207 cold-shock domain family protein (VIMSS) 18, 116
GSU0298 GSU0298 sigma-54 dependent DNA-binding response regulator, interruption-C (VIMSS) 116, 169
GSU0301 GSU0301 lytic murein transglycosylase, putative (VIMSS) 11, 197
GSU0333 atpE ATP synthase F0, C subunit (NCBI) 116, 170
GSU0390 GSU0390 conserved hypothetical protein (VIMSS) 11, 18
GSU0592 GSU0592 cytochrome c family protein (NCBI) 18, 116
GSU0652 nadE NAD+ synthetase (NCBI) 11, 197
GSU0654 moeB thiF family protein (NCBI) 11, 315
GSU0666 rpsR ribosomal protein S18 (NCBI) 26, 116
GSU0667 GSU0667 membrane protein, putative (VIMSS) 26, 116
GSU0906 rpsU-1 ribosomal protein S21 (NCBI) 11, 248
GSU0992 GSU0992 hypothetical protein (VIMSS) 11, 250
GSU1227 GSU1227 ABC transporter, ATP-binding protein (VIMSS) 11, 147
GSU1228 GSU1228 cytochrome c family protein (VIMSS) 11, 147
GSU1233 GSU1233 phosphoesterase, putative (NCBI) 11, 50
GSU1377 GSU1377 3-hydroxybutyryl-CoA dehydratase (VIMSS) 11, 126
GSU1515 thrS threonyl-tRNA synthetase (NCBI) 101, 116
GSU1518 rplT ribosomal protein L20 (NCBI) 56, 116
GSU1706 panC pantoate--beta-alanine ligase (NCBI) 11, 125
GSU1746 ihfB integration host factor, beta subunit (NCBI) 11, 265
GSU1749 GSU1749 hypothetical protein (VIMSS) 11, 70
GSU1905 GSU1905 cold shock domain family protein (VIMSS) 56, 116
GSU2021 pepQ-2 xaa-pro dipeptidase (NCBI) 11, 309
GSU2023 GSU2023 conserved hypothetical protein (VIMSS) 11, 262
GSU2287 GSU2287 response regulator (VIMSS) 11, 46
GSU2647 GSU2647 conserved hypothetical protein (VIMSS) 11, 147
GSU2727 GSU2727 hypothetical protein (VIMSS) 11, 147
GSU2830 rplQ ribosomal protein L17 (NCBI) 116, 340
GSU2833 rpsK ribosomal protein S11 (NCBI) 24, 116
GSU2837 secY preprotein translocase, SecY subunit (NCBI) 116, 333
GSU2860 fusA-3 translation elongation factor G (NCBI) 37, 116
GSU2867 rplK ribosomal protein L11 (NCBI) 58, 116
GSU2915 GSU2915 sigma-54 dependent DNA-binding response regulator (VIMSS) 11, 116
GSU3132 huP-2 DNA-binding protein HU (NCBI) 35, 116
GSU3237 GSU3237 hypothetical protein (VIMSS) 116, 238
GSU3294 GSU3294 rubredoxin-oxygen oxidoreductase, putative (VIMSS) 11, 258
GSU3318 GSU3318 conserved hypothetical protein (VIMSS) 11, 50
GSU3320 prmA ribosomal protein L11 methyltransferase, putative (NCBI) 11, 50
GSU3321 GSU3321 phosphoglucomutase/phosphomannomutase family protein (VIMSS) 11, 50
GSU3322 corA-2 magnesium and cobalt transport protein CorA (NCBI) 11, 50
GSU3405 GSU3405 amino acid ABC transporter, permease protein (VIMSS) 11, 18
GSU3454 GSU3454 radical SAM domain protein (NCBI) 60, 116
GSU3467 GSU3467 conserved hypothetical protein TIGR00278 (VIMSS) 116, 267
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 GSU2915
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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