Organism : Geobacter sulfurreducens | Module List :
GSU1626

transcriptional regulator, GntR family (VIMSS)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1626
(Mouseover regulator name to see its description)

GSU1626 is regulated by 20 influences and regulates 59 modules.
Regulators for GSU1626 (20)
Regulator Module Operator
GSU0366 136 tf
GSU0581 136 tf
GSU0655 136 tf
GSU0732 136 tf
GSU1522 136 tf
GSU1525 136 tf
GSU1626 136 tf
GSU1692 136 tf
GSU1727 136 tf
GSU1989 136 tf
GSU2524 136 tf
GSU2581 136 tf
GSU2831 136 tf
GSU1522 154 tf
GSU1626 154 tf
GSU2524 154 tf
GSU2831 154 tf
GSU2915 154 tf
GSU2926 154 tf
GSU3324 154 tf
Regulated by GSU1626 (59)
Module Residual Genes
2 0.28 15
6 0.45 23
14 0.36 20
18 0.48 21
19 0.53 7
27 0.51 26
42 0.50 21
43 0.30 13
49 0.44 26
63 0.48 19
67 0.33 21
73 0.57 12
74 0.28 16
85 0.45 18
92 0.31 17
96 0.45 25
107 0.49 25
109 0.39 22
136 0.37 16
147 0.48 28
154 0.32 15
156 0.31 16
159 0.51 19
162 0.44 18
163 0.34 18
165 0.45 21
168 0.28 15
170 0.40 17
175 0.42 16
176 0.50 18
178 0.33 20
182 0.26 12
183 0.47 30
186 0.50 22
192 0.30 16
199 0.42 18
207 0.50 22
212 0.42 21
218 0.32 18
220 0.45 20
227 0.36 14
236 0.62 23
241 0.44 21
245 0.37 17
246 0.34 17
257 0.49 25
259 0.30 15
261 0.32 16
270 0.37 15
277 0.45 15
291 0.45 16
294 0.36 19
299 0.26 18
310 0.45 19
311 0.42 15
312 0.37 17
316 0.29 16
328 0.27 14
339 0.27 13
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2432 1.30e+03 Tta.aat.C.Ctt.ttT.tac
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2433 1.20e+04 aCcGtaGcCaatCaGcacaAtCCt
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2468 2.50e+02 TtTTTtgTgTgG
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2469 4.20e+01 T.aAcaAAt..act.TAtt
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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 GSU1626

GSU1626 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for GSU1626

GSU1626 has total of 29 gene neighbors in modules 136, 154
Gene neighbors (29)
Gene Common Name Description Module membership
GSU0108 GSU0108 ATP synthase F0, B' subunit, putative (VIMSS) 154, 161
GSU0334 atpB ATP synthase F0, A subunit (NCBI) 62, 136
GSU0644 GSU0644 KH domain protein (VIMSS) 62, 154
GSU0647 GSU0647 conserved hypothetical protein (VIMSS) 154, 267
GSU0662 rplY ribosoma protein L25 (NCBI) 154, 161
GSU1110 ndk nucleoside diphosphate kinase (NCBI) 154, 161
GSU1246 dgt deoxyguanosinetriphosphate triphosphohydrolase, putative (NCBI) 75, 154
GSU1314 GSU1314 membrane protein, putative (VIMSS) 75, 136
GSU1516 infC translation initiation factor IF-3 (NCBI) 154, 161
GSU1521 ihfA-1 integration host factor, alpha subunit (NCBI) 154, 161
GSU1522 GSU1522 transcriptional regulator, putative (VIMSS) 154, 161
GSU1626 GSU1626 transcriptional regulator, GntR family (VIMSS) 136, 154
GSU1651 fbP-1 fructose-1,6-bisphosphatase (NCBI) 136, 154
GSU1738 GSU1738 indolepyruvate ferredoxin oxidoreductase, beta subunit (VIMSS) 112, 136
GSU1757 rimI ribosomal-protein-alanine acetyltransferase (VIMSS) 136, 208
GSU1804 pdxJ pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 67, 136
GSU1884 GSU1884 conserved hypothetical protein (VIMSS) 136, 263
GSU1903 leuC 3-isopropylmalate dehydratase, large subunit, putative (NCBI) 136, 197
GSU1919 pyrH uridylate kinase (NCBI) 154, 161
GSU1921 rpsB ribosomal protein S2 (NCBI) 154, 333
GSU1996 GSU1996 cytochrome c family protein (NCBI) 35, 154
GSU2028 GSU2028 type IV pilus biogenesis protein PilQ (VIMSS) 76, 136
GSU2029 GSU2029 lipoprotein, putative (VIMSS) 76, 136
GSU2519 GSU2519 (R)-2-hydroxyglutaryl-CoA dehydratase beta-subunit, putative (NCBI) 136, 168
GSU2642 GSU2642 cytochrome c family protein (NCBI) 136, 169
GSU2643 GSU2643 cytochrome c family protein (NCBI) 18, 136
GSU2644 GSU2644 hypothetical protein (VIMSS) 136, 330
GSU3236 rplU ribosomal protein L21 (NCBI) 37, 154
GSU3392 GSU3392 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 80, 136
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 GSU1626
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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