Organism : Geobacter sulfurreducens | Module List :
GSU2964 modE

molybdenum transport regulatory protein ModE (NCBI)

CircVis
Functional Annotations (9)
Function System
N-terminal domain of molybdenum-binding protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdate ion transport go/ biological_process
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
ModE_repress tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2964
(Mouseover regulator name to see its description)

GSU2964 is regulated by 17 influences and regulates 35 modules.
Regulators for GSU2964 modE (17)
Regulator Module Operator
GSU0041 187 tf
GSU1218 187 tf
GSU1831 187 tf
GSU2753 187 tf
GSU2817 187 tf
GSU2964 187 tf
GSU3041 187 tf
GSU0041 177 tf
GSU0178 177 tf
GSU0187 177 tf
GSU0366 177 tf
GSU0581 177 tf
GSU0732 177 tf
GSU1495 177 tf
GSU1525 177 tf
GSU1727 177 tf
GSU2964 177 tf

Warning: GSU2964 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
2514 1.10e+02 g.tctctccc.gCc.cttcatTtC
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2515 1.70e+04 T.TggCg.tTtcaTG
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2534 4.60e+00 GGcgATAtaCTt.at
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2535 2.10e+03 ggCcCaacGaCcagCcc.c.acAc
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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 GSU2964

GSU2964 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
N-terminal domain of molybdenum-binding protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdate ion transport go/ biological_process
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
ModE_repress tigr/ tigrfam
Module neighborhood information for GSU2964

GSU2964 has total of 33 gene neighbors in modules 177, 187
Gene neighbors (33)
Gene Common Name Description Module membership
GSU0071 GSU0071 hypothetical protein (VIMSS) 177, 216
GSU0142 pgpA phosphatidylglycerophosphatase A (NCBI) 187, 194
GSU0469 GSU0469 hypothetical protein (VIMSS) 41, 187
GSU0672 GSU0672 hypothetical protein (VIMSS) 177, 251
GSU0725 GSU0725 hypothetical protein (VIMSS) 150, 187
GSU0726 GSU0726 chemotaxis protein CheD, putative (VIMSS) 177, 279
GSU0746 GSU0746 cytochrome p460, putative (VIMSS) 134, 177
GSU0789 GSU0789 response regulator (VIMSS) 187, 299
GSU0804 WrbA trp repressor binding protein WrbA (NCBI) 2, 177
GSU1007 GSU1007 GAF domain/HD domain protein (NCBI) 177, 240
GSU1209 GSU1209 conserved hypothetical protein (VIMSS) 177, 188
GSU1557 GSU1557 mechanosensitive ion channel family protein (NCBI) 123, 187
GSU1559 GSU1559 hypothetical protein (VIMSS) 123, 177
GSU1669 GSU1669 hypothetical protein (VIMSS) 123, 177
GSU2437 GSU2437 conserved hypothetical protein (VIMSS) 3, 187
GSU2528 GSU2528 conserved domain protein (NCBI) 2, 177
GSU2583 GSU2583 isochorismatase family protein (NCBI) 123, 187
GSU2793 GSU2793 hypothetical protein (VIMSS) 114, 187
GSU2794 mscL large conductance mechanosensitive channel protein (NCBI) 187, 194
GSU2800 draG dinitrogenase reductase activating glycohydrolase (NCBI) 150, 187
GSU2817 GSU2817 transcriptional regulator, LysR family (VIMSS) 187, 193
GSU2823 GSU2823 HlyD family secretion protein (NCBI) 177, 187
GSU2963 modD additional component of molybdate ABC transporter (Dmitry Rodionov) 150, 187
GSU2964 modE molybdenum transport regulatory protein ModE (NCBI) 177, 187
GSU3328 GSU3328 conserved hypothetical protein (NCBI) 177, 270
GSU3329 GSU3329 radical SAM domain protein (NCBI) 2, 177
GSU3341 GSU3341 hypothetical protein (NCBI) 134, 177
GSU3342 GSU3342 conserved domain protein (NCBI) 177, 279
GSU3343 GSU3343 SpoVR-like family protein (NCBI) 177, 240
GSU3351 GSU3351 hypothetical protein (VIMSS) 123, 187
GSU3438 GSU3438 conserved hypothetical protein (VIMSS) 187, 299
GSU3440 GSU3440 hypothetical protein (VIMSS) 167, 187
GSU3462 GSU3462 lipoprotein, putative (VIMSS) 187, 216
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 GSU2964
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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