Organism : Geobacter sulfurreducens | Module List :
GSU0164

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0164
(Mouseover regulator name to see its description)

GSU0164 is regulated by 14 influences and regulates 23 modules.
Regulators for GSU0164 (14)
Regulator Module Operator
GSU1639 315 tf
GSU1905 315 tf
GSU2041 315 tf
GSU2625 315 tf
GSU2831 315 tf
GSU3387 315 tf
GSU0147 113 tf
GSU0205 113 tf
GSU0254 113 tf
GSU0473 113 tf
GSU0836 113 tf
GSU2587 113 tf
GSU2915 113 tf
GSU3324 113 tf

Warning: GSU0164 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
2386 5.30e+02 taTtaTaaatatTTgaaACtAaa
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2387 3.20e+03 Aa.CAattGTtaaTtGaaAacA
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2786 6.00e+01 tTcAtaT.atT
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2787 4.00e+03 AaAaAAcAcAagTT
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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 GSU0164

GSU0164 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU0164

GSU0164 has total of 48 gene neighbors in modules 113, 315
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0164 GSU0164 conserved hypothetical protein (VIMSS) 113, 315
GSU0352 psaD thiol peroxidase (NCBI) 130, 315
GSU0353 GSU0353 membrane protein, putative (NCBI) 314, 315
GSU0354 GSU0354 conserved hypothetical protein (VIMSS) 113, 286
GSU0654 moeB thiF family protein (NCBI) 11, 315
GSU0657 GSU0657 hypothetical protein (VIMSS) 53, 315
GSU0777 fdnG formate dehydrogenase, major subunit, selenocysteine-containing (NCBI) 113, 184
GSU0861 GSU0861 conserved hypothetical protein (NCBI) 113, 144
GSU0886 GSU0886 radical SAM domain protein (NCBI) 113, 336
GSU1249 GSU1249 sensory box histidine kinase (VIMSS) 40, 113
GSU1386 GSU1386 conserved hypothetical protein (VIMSS) 18, 315
GSU1503 GSU1503 glycosyl transferase, group 2 family protein (VIMSS) 103, 315
GSU1584 bioB biotin synthetase (Dmitry Rodionov) 120, 315
GSU1610 GSU1610 efflux transporter, RND family, MFP subunit (NCBI) 113, 258
GSU1631 GSU1631 metallo-beta-lactamase family protein (VIMSS) 81, 315
GSU1639 GSU1639 Rrf2 family protein (NCBI) 264, 315
GSU1640 cydA cytochrome d ubiquinol oxidase, subunit I (NCBI) 264, 315
GSU1641 cydB cytochrome d ubiquinol oxidase, subunit II (NCBI) 264, 315
GSU1675 GSU1675 hypothetical protein (VIMSS) 113, 123
GSU1766 xseB exodeoxyribonuclease VII, small subunit (NCBI) 113, 258
GSU1769 GSU1769 conserved hypothetical protein (VIMSS) 97, 113
GSU1906 leuA 2-isopropylmalate synthase (NCBI) 137, 315
GSU1999 hfq hfq protein (NCBI) 42, 315
GSU2014 GSU2014 hypothetical protein (VIMSS) 108, 315
GSU2096 GSU2096 iron-sulfur cluster-binding protein (VIMSS) 113, 322
GSU2132 GSU2132 hypothetical protein (VIMSS) 113, 275
GSU2133 GSU2133 lipoprotein, putative (VIMSS) 113, 190
GSU2134 GSU2134 nitrogen regulatory protein P-II, putative (VIMSS) 113, 190
GSU2135 GSU2135 heavy metal efflux pump, CzcA family (VIMSS) 59, 113
GSU2136 GSU2136 heavy metal efflux pump, CzcB family (VIMSS) 113, 155
GSU2176 GSU2176 hypothetical protein (VIMSS) 113, 190
GSU2177 GSU2177 hypothetical protein (VIMSS) 113, 181
GSU2405 GSU2405 hypothetical protein (VIMSS) 113, 325
GSU2553 GSU2553 glycosyl transferase, group 2 family protein (VIMSS) 231, 315
GSU2689 GSU2689 hypothetical protein (VIMSS) 113, 157
GSU2720 hoxU NAD-reducing hydrogenase, gamma subunit (NCBI) 113, 336
GSU2730 GSU2730 hypothetical protein (NCBI) 113, 264
GSU2764 GSU2764 hypothetical protein (VIMSS) 42, 113
GSU2844 rpsN ribosomal protein S14 (NCBI) 315, 340
GSU2906 GSU2906 conserved hypothetical protein (VIMSS) 13, 113
GSU3098 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 203, 315
GSU3107 rpmE ribosomal protein L31 (NCBI) 113, 140
GSU3215 GSU3215 hypothetical protein (VIMSS) 113, 140
GSU3246 GSU3246 thioredoxin peroxidase (VIMSS) 264, 315
GSU3259 GSU3259 cytochrome c family protein (NCBI) 42, 113
GSU3293 GSU3293 conserved hypothetical protein (VIMSS) 35, 315
GSU3345 GSU3345 hypothetical protein (VIMSS) 113, 157
GSU3466 GSU3466 membrane protein, putative (VIMSS) 230, 315
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 GSU0164
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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