Organism : Geobacter sulfurreducens | Module List :
GSU2364 rfbA

mannose-6-phosphate isomerase (NCBI)

CircVis
Functional Annotations (7)
Function System
Mannose-6-phosphate isomerase cog/ cog
polysaccharide metabolic process go/ biological_process
mannose-1-phosphate guanylyltransferase (GDP) activity go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2364
(Mouseover regulator name to see its description)

GSU2364 is regulated by 23 influences and regulates 0 modules.
Regulators for GSU2364 rfbA (23)
Regulator Module Operator
GSU0013 156 tf
GSU0205 156 tf
GSU0399 156 tf
GSU0473 156 tf
GSU0735 156 tf
GSU0770 156 tf
GSU1410 156 tf
GSU1626 156 tf
GSU1989 156 tf
GSU2523 156 tf
GSU2587 156 tf
GSU2915 156 tf
GSU3387 156 tf
GSU0205 112 tf
GSU0473 112 tf
GSU0812 112 tf
GSU1115 112 tf
GSU1410 112 tf
GSU1617 112 tf
GSU1727 112 tf
GSU2581 112 tf
GSU3396 112 tf
GSU3457 112 tf

Warning: GSU2364 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
2384 5.80e+03 tCcggcgCcgcaa.gGggtaA
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2385 2.80e+04 ttcTtTTaTTg
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2472 3.30e+03 TgacGGgcCGttTtcccT
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2473 1.90e+04 GCat.TAaTtTAat.gGTTt
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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 GSU2364

GSU2364 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Mannose-6-phosphate isomerase cog/ cog
polysaccharide metabolic process go/ biological_process
mannose-1-phosphate guanylyltransferase (GDP) activity go/ molecular_function
Fructose and mannose metabolism kegg/ kegg pathway
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for GSU2364

GSU2364 has total of 35 gene neighbors in modules 112, 156
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0154 GSU0154 mutT/nudix family protein (NCBI) 112, 289
GSU0205 GSU0205 transcriptional regulator, TetR family (VIMSS) 112, 289
GSU0237 GSU0237 MaoC-like domain protein (NCBI) 156, 333
GSU0365 cyd-2 cytochrome c3 (NCBI) 52, 156
GSU0370 GSU0370 hypothetical protein (VIMSS) 144, 156
GSU0400 GSU0400 methyl-accepting chemotaxis protein (VIMSS) 82, 156
GSU0483 GSU0483 exsB protein (VIMSS) 112, 289
GSU0540 GSU0540 hypothetical protein (NCBI) 142, 156
GSU1005 nifR3 dihydrouridine synthase family protein (NCBI) 112, 333
GSU1067 GSU1067 conserved hypothetical protein (VIMSS) 156, 183
GSU1080 GSU1080 hypothetical protein (VIMSS) 112, 206
GSU1180 ftsH-1 cell division protein FtsH (NCBI) 112, 126
GSU1194 GSU1194 transporter, LysE family (VIMSS) 67, 112
GSU1410 GSU1410 conserved hypothetical protein (VIMSS) 112, 202
GSU1704 GSU1704 methyl-accepting chemotaxis protein, putative (VIMSS) 156, 329
GSU1738 GSU1738 indolepyruvate ferredoxin oxidoreductase, beta subunit (VIMSS) 112, 136
GSU1832 GSU1832 conserved hypothetical protein (NCBI) 112, 289
GSU1997 GSU1997 PDZ domain protein (NCBI) 156, 333
GSU2083 rfbA glucose-1-phosphate thymidylyltransferase (NCBI) 112, 333
GSU2213 GSU2213 GAF domain protein (VIMSS) 47, 112
GSU2364 rfbA mannose-6-phosphate isomerase (NCBI) 112, 156
GSU2464 GSU2464 hypothetical protein (VIMSS) 156, 183
GSU2565 GSU2565 sensor histidine kinase (VIMSS) 112, 156
GSU2567 GSU2567 sensor histidine kinase (VIMSS) 112, 144
GSU2589 GSU2589 hypothetical protein (VIMSS) 156, 190
GSU2600 GSU2600 None 156, 333
GSU2651 GSU2651 amino acid ABC transporter, ATP-binding protein (VIMSS) 13, 156
GSU2722 GSU2722 NAD-reducing hydrogenase, putative (VIMSS) 112, 128
GSU2862 GSU2862 None 156, 231
GSU2990 cobD cobalamin biosynthesis protein CobD (NCBI) 112, 289
GSU2994 cobM precorrin-4 C11-methyltransferase (NCBI) 153, 156
GSU3080 GSU3080 hypothetical protein (VIMSS) 112, 207
GSU3113 GSU3113 metallo-beta-lactamase family protein (VIMSS) 112, 128
GSU3383 gatC glutamyl-tRNA(Gln) amidotransferase, C subunit (NCBI) 112, 289
GSU3457 GSU3457 glycine cleavage system transcriptional repressor, putative (VIMSS) 112, 289
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 GSU2364
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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