Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2204 tnaA

tryptophanase

CircVis
Functional Annotations (6)
Function System
Tryptophanase cog/ cog
tryptophanase activity go/ molecular_function
aromatic amino acid family metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Tryptophan metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2204
(Mouseover regulator name to see its description)

DVU2204 is regulated by 18 influences and regulates 0 modules.
Regulators for DVU2204 tnaA (18)
Regulator Module Operator
DVU0653 284 tf
DVU0653
DVU1744
284 combiner
DVU1517 284 tf
DVU2633
DVU1744
284 combiner
DVU2690 284 tf
DVU2886
DVU1754
284 combiner
DVUA0024 284 tf
DVUA0057 284 tf
DVUA0143 284 tf
DVU0030
DVU0525
133 combiner
DVU0230 133 tf
DVU0230
DVU1083
133 combiner
DVU0525 133 tf
DVU0653
DVU2251
133 combiner
DVU1754
DVU0030
133 combiner
DVU1754
DVU2785
133 combiner
DVU1967 133 tf
DVU2036
DVU2251
133 combiner

Warning: DVU2204 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
257 1.00e-06 aGgagaAggGa.ggcagttcaaGC
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RegPredict
258 3.70e-04 aAaGGaaAAGaCAAccGCCTtcCA
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RegPredict
543 7.00e+01 gC.CacCATCc
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RegPredict
544 5.00e+02 gCCttCGgCAacGtc
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RegPredict
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 DVU2204

DVU2204 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Tryptophanase cog/ cog
tryptophanase activity go/ molecular_function
aromatic amino acid family metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Tryptophan metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Module neighborhood information for DVU2204

DVU2204 has total of 37 gene neighbors in modules 133, 284
Gene neighbors (37)
Gene Common Name Description Module membership
DVU0008 hypothetical protein DVU0008 39, 284
DVU0181 modB molybdenum ABC transporter permease 284, 329
DVU0185 hypothetical protein DVU0185 284, 299
DVU0283 AhpF family protein/thioredoxin reductase 284, 329
DVU0529 Rrf2 family transcriptional regulator 133, 189
DVU0530 response regulator, rrf1 protein 133, 189
DVU0531 hmc operon protein 6 133, 189
DVU0532 hmc operon protein 5 133, 189
DVU0535 hmc operon protein 2 133, 189
DVU0536 hmcA high-molecular-weight cytochrome C 133, 189
DVU0877 hypothetical protein DVU0877 160, 284
DVU0878 dnaK suppressor protein 133, 202
DVU0926 hypothetical protein DVU0926 133, 244
DVU0929 obgE GTPase ObgE 133, 244
DVU0930 proB gamma-glutamyl kinase 30, 133
DVU1416 hypothetical protein DVU1416 284, 329
DVU1505 holin 133, 152
DVU1506 hypothetical protein DVU1506 133, 152
DVU1755 hypothetical protein DVU1755 118, 133
DVU1899 DNA repair protein RecO 25, 284
DVU2147 L-serine dehydratase 68, 284
DVU2204 tnaA tryptophanase 133, 284
DVU2303 hypothetical protein DVU2303 51, 284
DVU2334 hypothetical protein DVU2334 284, 329
DVU2346 hypothetical protein DVU2346 284, 329
DVU2814 hypothetical protein DVU2814 133, 256
DVU2815 outer membrane efflux protein 133, 256
DVU2816 multidrug resistance protein 133, 256
DVU2817 multidrug resistance protein 133, 256
DVU2818 hypothetical protein DVU2818 133, 256
DVU2819 TetR family transcriptional regulator 133, 256
DVU3000 hypothetical protein DVU3000 15, 284
DVU3007 hypothetical protein DVU3007 15, 284
DVU3034 hypothetical protein DVU3034 36, 284
DVU3057 oxygen-independent coproporphyrinogen III oxidase 82, 284
DVU3214 phosphoenolpyruvate synthase-like protein 67, 284
DVU3280 None 7, 133
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 DVU2204
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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