Organism : Geobacter sulfurreducens | Module List :
GSU2561

conserved domain protein (NCBI)

CircVis
Functional Annotations (2)
Function System
nucleotide binding go/ molecular_function
protein binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2561
(Mouseover regulator name to see its description)

GSU2561 is regulated by 14 influences and regulates 0 modules.
Regulators for GSU2561 (14)
Regulator Module Operator
GSU1277 95 tf
GSU1569 95 tf
GSU1940 95 tf
GSU2716 95 tf
GSU2787 95 tf
GSU2987 95 tf
GSU3229 95 tf
GSU3370 95 tf
GSU0041 193 tf
GSU1345 193 tf
GSU2262 193 tf
GSU2809 193 tf
GSU2817 193 tf
GSU2964 193 tf

Warning: GSU2561 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
2350 2.70e+03 GgAGGTGg
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2351 4.30e+03 tCAaaAAAAATGC
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2546 1.10e+02 aaAAATTCAc
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2547 2.70e+03 GtaAtAAaAaTtgtTatgatC
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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 GSU2561

GSU2561 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
nucleotide binding go/ molecular_function
protein binding go/ molecular_function
Module neighborhood information for GSU2561

GSU2561 has total of 51 gene neighbors in modules 95, 193
Gene neighbors (51)
Gene Common Name Description Module membership
GSU0061 GSU0061 hypothetical protein (VIMSS) 9, 95
GSU0116 GSU0116 transglycosylase (VIMSS) 95, 200
GSU0214 GSU0214 conserved hypothetical protein (VIMSS) 6, 95
GSU0357 GSU0357 cytochrome c family protein (VIMSS) 6, 95
GSU0533 GSU0533 cytochrome c family protein, putative (NCBI) 54, 95
GSU0640 GSU0640 conserved hypothetical protein (VIMSS) 95, 158
GSU0707 sugE sugE protein (NCBI) 95, 234
GSU0714 GSU0714 hypothetical protein (VIMSS) 193, 288
GSU0716 GSU0716 hypothetical protein (NCBI) 65, 193
GSU0806 citG ATP:dephospho-CoA triphosphoribosyl transferase (NCBI) 95, 133
GSU0843 GSU0843 NADH oxidase, putative (VIMSS) 9, 95
GSU0845 GSU0845 Rieske 2Fe-2S family protein (VIMSS) 9, 95
GSU0926 GSU0926 mce-related protein (NCBI) 20, 95
GSU0942 suhB inositol-1-monophosphatase (NCBI) 157, 193
GSU1255 GSU1255 conserved hypothetical protein (NCBI) 95, 104
GSU1256 GSU1256 conserved domain protein (NCBI) 6, 95
GSU1404 GSU1404 radical SAM domain protein (NCBI) 171, 193
GSU1608 GSU1608 hypothetical protein (VIMSS) 193, 235
GSU1650 GSU1650 cytochrome b/b6 complex, iron-sulfur subunit (VIMSS) 193, 310
GSU1670 GSU1670 lipoprotein, putative (VIMSS) 123, 193
GSU1844 GSU1844 IPT/TIG domain protein, putative (VIMSS) 9, 95
GSU1995 GSU1995 hypothetical protein (VIMSS) 193, 216
GSU2193 GSU2193 conserved hypothetical protein (VIMSS) 4, 193
GSU2199 GSU2199 conserved hypothetical protein (VIMSS) 95, 273
GSU2319 GSU2319 conserved hypothetical protein (VIMSS) 193, 310
GSU2472 vapC virulence associated protein C (NCBI) 181, 193
GSU2473 vapB virulence associated protein B (NCBI) 193, 216
GSU2509 GSU2509 glycosyl transferase, group 2 family protein (VIMSS) 9, 95
GSU2515 GSU2515 cytochrome c family protein, putative (NCBI) 9, 95
GSU2561 GSU2561 conserved domain protein (NCBI) 95, 193
GSU2640 GSU2640 hypothetical protein (VIMSS) 66, 95
GSU2641 GSU2641 hypothetical protein (VIMSS) 66, 95
GSU2742 GSU2742 hypothetical protein (VIMSS) 65, 193
GSU2743 GSU2743 cytochrome c family protein (VIMSS) 65, 193
GSU2771 GSU2771 conserved hypothetical protein (VIMSS) 193, 202
GSU2775 GSU2775 hypothetical protein (VIMSS) 9, 95
GSU2787 GSU2787 transcriptional regulator, LysR family (VIMSS) 95, 224
GSU2809 GSU2809 transcriptional regulator, Fur family (VIMSS) 193, 216
GSU2817 GSU2817 transcriptional regulator, LysR family (VIMSS) 187, 193
GSU2896 GSU2896 ankyrin-related protein (VIMSS) 6, 95
GSU2967 GSU2967 hypothetical protein (VIMSS) 86, 193
GSU2986 znuA periplasmic component of zinc ABC transporter (Dmitry Rodionov) 193, 202
GSU2988 GSU2988 conserved hypothetical protein (VIMSS) 45, 193
GSU3048 flgH flagellar L-ring protein FlgH (NCBI) 95, 186
GSU3071 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI) 95, 264
GSU3128 GSU3128 hypothetical protein (VIMSS) 95, 183
GSU3238 GSU3238 Rieske 2Fe-2S family protein (VIMSS) 95, 264
GSU3272 GSU3272 hypothetical protein (VIMSS) 193, 241
GSU3273 GSU3273 hypothetical protein (VIMSS) 193, 241
GSU3274 GSU3274 cytochrome c family protein, putative (NCBI) 193, 241
GSU3368 ispD 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (NCBI) 159, 193
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 GSU2561
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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