Organism : Geobacter sulfurreducens | Module List :
GSU2379 trpB

pyridoxal-phosphate dependent enzyme (NCBI)

CircVis
Functional Annotations (9)
Function System
Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) cog/ cog
tryptophan biosynthetic process go/ biological_process
tryptophan synthase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
trpB_rel tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2379
(Mouseover regulator name to see its description)

GSU2379 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU2379 trpB (18)
Regulator Module Operator
GSU0359 93 tf
GSU0896 93 tf
GSU1072 93 tf
GSU1483 93 tf
GSU2587 93 tf
GSU2868 93 tf
GSU2964 93 tf
GSU3087 93 tf
GSU0041 196 tf
GSU1320 196 tf
GSU1569 196 tf
GSU1992 196 tf
GSU2262 196 tf
GSU2666 196 tf
GSU2809 196 tf
GSU2964 196 tf
GSU3041 196 tf
GSU3324 196 tf

Warning: GSU2379 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
2346 1.90e-05 GagGCtaAAaGtAAAaAttCC
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2347 6.80e-05 TAcaatcCCccgGtTTgActtcca
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2552 2.20e+02 tGaAAA
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2553 3.70e+02 TaaaaAaAagtgaAaatTTaT
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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 GSU2379

GSU2379 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) cog/ cog
tryptophan biosynthetic process go/ biological_process
tryptophan synthase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
trpB_rel tigr/ tigrfam
Module neighborhood information for GSU2379

GSU2379 has total of 35 gene neighbors in modules 93, 196
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0085 GSU0085 heterodisulfide reductase, cytochrome reductase subunit (VIMSS) 8, 196
GSU0139 GSU0139 hypothetical protein (VIMSS) 93, 311
GSU0160 dapB dihydrodipicolinate reductase (NCBI) 196, 334
GSU0229 alkK medium-chain-fatty-acid--CoA ligase (NCBI) 32, 93
GSU0326 gspG general secretion pathway protein G (NCBI) 93, 143
GSU0486 ilvA threonine dehydratase (NCBI) 196, 239
GSU0797 GSU0797 conserved hypothetical protein TIGR00427 (VIMSS) 196, 308
GSU0798 GSU0798 amino acid ABC transporter, ATP-binding protein (VIMSS) 111, 196
GSU0799 GSU0799 amino acid ABC transporter, permease protein (NCBI) 196, 224
GSU0944 metC-1 cystathionine beta-lyase (NCBI) 93, 223
GSU0945 metC-2 cystathionine beta-lyase (NCBI) 93, 223
GSU0946 GSU0946 sensory box/GGDEF family protein (VIMSS) 32, 93
GSU0966 GSU0966 hypothetical protein (VIMSS) 32, 93
GSU1021 GSU1021 hypothetical protein (VIMSS) 93, 142
GSU1022 GSU1022 hypothetical protein (VIMSS) 93, 155
GSU1023 glgA-1 glycogen synthase (NCBI) 31, 93
GSU1089 GSU1089 iron-sulfur cluster-binding protein (VIMSS) 196, 239
GSU1210 GSU1210 metallo-beta-lactamase family protein (NCBI) 174, 196
GSU1328 GSU1328 conserved hypothetical protein (VIMSS) 80, 196
GSU1537 exeA general secretion pathway protein-related protein (NCBI) 196, 334
GSU1602 fabD malonyl CoA-acyl carrier protein transacylase (NCBI) 93, 209
GSU1695 thrC threonine synthase (NCBI) 131, 196
GSU1756 GSU1756 dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) 174, 196
GSU1803 acpS holo-(acyl-carrier-protein) synthase (NCBI) 67, 196
GSU1933 fusA-1 translation elongation factor G (NCBI) 174, 196
GSU2378 trpF N-(5'phosphoribosyl)anthranilate isomerase (NCBI) 131, 196
GSU2379 trpB pyridoxal-phosphate dependent enzyme (NCBI) 93, 196
GSU2380 trpC Indole-3-glycerol phosphate synthase (NCBI) 29, 196
GSU2381 trpD anthranilate phosphoribosyltransferase (NCBI) 80, 196
GSU2382 trpG anthranilate synthase component II (NCBI) 47, 196
GSU2383 trpE anthranilate synthase component I (NCBI) 131, 196
GSU2462 metA homoserine O-acetyltransferase (NCBI) 32, 93
GSU2944 GSU2944 (R)-2-hydroxyglutaryl-CoA dehydratase alpha-subunit, putative (VIMSS) 32, 93
GSU2945 GSU2945 (R)-2-hydroxyglutaryl-CoA dehydratase activator, putative (VIMSS) 32, 93
GSU2982 GSU2982 TonB dependent receptor, putative (VIMSS) 32, 93
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 GSU2379
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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