Organism : Geobacter sulfurreducens | Module List :
GSU0187

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
metal ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0187
(Mouseover regulator name to see its description)

GSU0187 is regulated by 17 influences and regulates 33 modules.
Regulators for GSU0187 (17)
Regulator Module Operator
GSU0031 240 tf
GSU0187 240 tf
GSU0581 240 tf
GSU1201 240 tf
GSU1525 240 tf
GSU1831 240 tf
GSU2753 240 tf
GSU2964 240 tf
GSU3396 240 tf
GSU0175 237 tf
GSU0187 237 tf
GSU0581 237 tf
GSU1003 237 tf
GSU1934 237 tf
GSU2033 237 tf
GSU2753 237 tf
GSU3206 237 tf

Warning: GSU0187 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
2634 5.70e+01 cggGcCGgTaTtTTC
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2635 4.00e+02 cGC.GgggCGg
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2640 9.20e+02 tCa..gcGCaG
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2641 9.30e+03 TActaCAAaAA
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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 GSU0187

GSU0187 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
metal ion binding go/ molecular_function
Module neighborhood information for GSU0187

GSU0187 has total of 31 gene neighbors in modules 237, 240
Gene neighbors (31)
Gene Common Name Description Module membership
GSU0084 GSU0084 aminotransferase, classes I and II (NCBI) 3, 237
GSU0173 GSU0173 conserved hypothetical protein (VIMSS) 194, 240
GSU0187 GSU0187 conserved hypothetical protein (VIMSS) 237, 240
GSU0219 GSU0219 cytochrome c oxidase, subunit I (VIMSS) 49, 237
GSU0221 GSU0221 cytochrome c oxidase, subunit IV (VIMSS) 49, 237
GSU0711 GSU0711 endonuclease/exonuclease/phosphatase family protein (NCBI) 194, 240
GSU0909 GSU0909 pyridine nucleotide-disulphide oxidoreductase family protein (NCBI) 138, 237
GSU0918 GSU0918 S-adenosylmethionine synthetase family protein (NCBI) 49, 240
GSU1007 GSU1007 GAF domain/HD domain protein (NCBI) 177, 240
GSU1014 GSU1014 smr domain protein (VIMSS) 234, 240
GSU1399 corA-1 magnesium and cobalt transport protein CorA (NCBI) 234, 240
GSU1560 GSU1560 radical SAM domain protein (NCBI) 138, 240
GSU1726 GSU1726 hypothetical protein (VIMSS) 195, 240
GSU1728 GSU1728 conserved hypothetical protein (VIMSS) 123, 240
GSU1747 GSU1747 hypothetical protein (VIMSS) 127, 240
GSU2292 ald alanine dehydrogenase (NCBI) 123, 240
GSU2351 GSU2351 cation-transport ATPase, E1-E2 family (VIMSS) 49, 237
GSU2436 GSU2436 dehydrogenase complex, E1 component, beta subunit (NCBI) 182, 237
GSU2449 sucA 2-oxoglutarate dehydrogenase, E1 component (NCBI) 182, 237
GSU2584 GSU2584 lipoprotein, putative (VIMSS) 138, 237
GSU2649 GSU2649 amino acid ABC transporter, amino acid-binding protein (VIMSS) 237, 240
GSU2650 GSU2650 amino acid ABC transporter, permease protein, putative (VIMSS) 49, 237
GSU2655 pdhB pyruvate dehydrogenase complex E1 component, beta subunit (NCBI) 240, 258
GSU2724 GSU2724 cytochrome c family protein (NCBI) 23, 237
GSU2725 GSU2725 cytochrome c family protein (VIMSS) 23, 237
GSU2726 GSU2726 hypothetical protein (VIMSS) 133, 237
GSU2758 uvrA excinuclease ABC family protein (NCBI) 240, 327
GSU3331 pyk pyruvate kinase (NCBI) 237, 256
GSU3343 GSU3343 SpoVR-like family protein (NCBI) 177, 240
GSU3352 GSU3352 hypothetical protein (VIMSS) 237, 240
GSU3448 ackA-2 acetate kinase (NCBI) 23, 237
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 GSU0187
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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