Organism : Geobacter sulfurreducens | Module List :
GSU2612

rubrerythrin/rubredoxin protein, putative (VIMSS)

CircVis
Functional Annotations (5)
Function System
Rubrerythrin cog/ cog
phosphopyruvate hydratase activity go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
transition metal ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2612
(Mouseover regulator name to see its description)

GSU2612 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU2612 (19)
Regulator Module Operator
GSU0041 334 tf
GSU0359 334 tf
GSU1218 334 tf
GSU1320 334 tf
GSU1495 334 tf
GSU3041 334 tf
GSU3045 334 tf
GSU3060 334 tf
GSU3089 334 tf
GSU3324 334 tf
GSU0031 332 tf
GSU0041 332 tf
GSU0732 332 tf
GSU1218 332 tf
GSU1320 332 tf
GSU2753 332 tf
GSU2964 332 tf
GSU3041 332 tf
GSU3045 332 tf

Warning: GSU2612 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
2820 1.90e+03 ggcgaTt.TT.tcaa
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2821 1.30e+04 AtGTtCcGCT
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2824 6.60e-04 GgCAaggAaAA
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2825 4.90e+02 at..Ttaac.tTT.ttaAAcg
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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 GSU2612

GSU2612 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Rubrerythrin cog/ cog
phosphopyruvate hydratase activity go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
transition metal ion binding go/ molecular_function
Module neighborhood information for GSU2612

GSU2612 has total of 29 gene neighbors in modules 332, 334
Gene neighbors (29)
Gene Common Name Description Module membership
GSU0020 GSU0020 hexapeptide transferase family protein (VIMSS) 174, 332
GSU0160 dapB dihydrodipicolinate reductase (NCBI) 196, 334
GSU0319 GSU0319 hypothetical protein (VIMSS) 143, 332
GSU0320 GSU0320 hypothetical protein (VIMSS) 28, 332
GSU0321 GSU0321 general secretion pathway protein L, putative (NCBI) 218, 334
GSU0322 gspK general secretion pathway protein K (NCBI) 143, 334
GSU0323 GSU0323 general secretion pathway protein j, putative (NCBI) 143, 334
GSU0324 GSU0324 general secretion pathway protein I, putative (NCBI) 143, 332
GSU0328 gspE general secretion pathway protein E (NCBI) 67, 334
GSU0999 GSU0999 acyl-(acyl-carrier-protein)--UDP-N- acetylglucosamine O-acyltransferase, putative (NCBI) 204, 332
GSU1000 GSU1000 conserved hypothetical protein (VIMSS) 328, 332
GSU1127 GSU1127 hypothetical protein (VIMSS) 144, 334
GSU1128 GSU1128 conserved hypothetical protein (VIMSS) 144, 334
GSU1132 ftsY cell division protein FtsY (NCBI) 204, 332
GSU1206 GSU1206 HDIG domain protein (NCBI) 98, 334
GSU1244 GSU1244 methyltransferase, putative (VIMSS) 67, 334
GSU1536 GSU1536 hypothetical protein (VIMSS) 144, 334
GSU1537 exeA general secretion pathway protein-related protein (NCBI) 196, 334
GSU1606 GSU1606 ribose 5-phosphate isomerase B, putative (VIMSS) 209, 334
GSU1812 argS arginyl-tRNA synthetase (NCBI) 52, 332
GSU1828 GSU1828 chorismate mutase domain protein (NCBI) 332, 334
GSU1829 GSU1829 hypothetical protein (NCBI) 204, 332
GSU1930 mglA1 GTP-binding domain protein (NCBI) 174, 332
GSU1931 GSU1931 hypothetical protein (VIMSS) 239, 332
GSU1932 GSU1932 hypothetical protein (VIMSS) 63, 332
GSU2266 lpxD UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase (VIMSS) 67, 334
GSU2275 GSU2275 conserved hypothetical protein (VIMSS) 29, 334
GSU2612 GSU2612 rubrerythrin/rubredoxin protein, putative (VIMSS) 332, 334
GSU3164 GSU3164 hypothetical protein (VIMSS) 222, 334
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 GSU2612
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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