Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1585

vitamin B12-dependent methionine synthase

CircVis
Functional Annotations (12)
Function System
Methionine synthase I, cobalamin-binding domain cog/ cog
dihydropteroate synthase activity go/ molecular_function
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
folic acid-containing compound biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
metal ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1585
(Mouseover regulator name to see its description)

DVU1585 is regulated by 11 influences and regulates 0 modules.
Regulators for DVU1585 (11)
Regulator Module Operator
DVU0653 294 tf
DVU0682
DVU1949
294 combiner
DVU0854
DVU0682
294 combiner
DVU0854
DVU2275
294 combiner
DVU1584
DVU0653
294 combiner
DVU2394
DVU2832
294 combiner
DVU2423
DVU2832
294 combiner
DVU3167 294 tf
DVU1572 12 tf
DVU1584 12 tf
DVU1584
DVU0269
12 combiner

Warning: DVU1585 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
23 5.00e-05 aAgGttTttca
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RegPredict
24 2.80e-01 attag.AcAaacatA.acTaTaCC
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RegPredict
563 9.90e-01 a.gtctTaTatttcTcc.T.ttat
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RegPredict
564 5.40e+00 cCtgAAAaaCa
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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 DVU1585

DVU1585 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Methionine synthase I, cobalamin-binding domain cog/ cog
dihydropteroate synthase activity go/ molecular_function
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
folic acid-containing compound biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
metal ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for DVU1585

DVU1585 has total of 39 gene neighbors in modules 12, 294
Gene neighbors (39)
Gene Common Name Description Module membership
DVU0709 hypothetical protein DVU0709 12, 92
DVU0783 hypothetical protein DVU0783 12, 219
DVU0785 rodA rod shape-determining protein RodA 75, 294
DVU0915 hypothetical protein DVU0915 12, 244
DVU1048 ccmB cytochrome c-type biogenesis protein CcmB 12, 251
DVU1062 hypothetical protein DVU1062 12, 29
DVU1100 tail fiber protein 12, 161
DVU1214 dolichyl-phosphate-mannose-protein mannosyltransferase family protein 65, 294
DVU1281 hypothetical protein DVU1281 95, 294
DVU1530 metallo-beta-lactamase family protein 12, 139
DVU1536 Slt family transglycosylase 12, 304
DVU1577 hslV ATP-dependent protease peptidase subunit 12, 226
DVU1580 ribose 5-phosphate isomerase 57, 294
DVU1581 hypothetical protein DVU1581 141, 294
DVU1583 hypothetical protein 282, 294
DVU1585 vitamin B12-dependent methionine synthase 12, 294
DVU1586 thioredoxin family protein 292, 294
DVU1588 hpt hypoxanthine phosphoribosyltransferase 215, 294
DVU1589 hypothetical protein DVU1589 12, 294
DVU1605 uvrB excinuclease ABC subunit B 12, 330
DVU1680 suhB inositol-1-monophosphatase 12, 226
DVU1687 glycosyl transferase group 2 family protein 12, 318
DVU1769 hydA periplasmic 176, 294
DVU1770 hydB periplasmic 137, 294
DVU1775 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 12, 94
DVU1803 glycosyl transferase group 1 family protein 12, 198
DVU1866 hypothetical protein DVU1866 292, 294
DVU1881 phoH family protein 12, 249
DVU1900 hypothetical protein DVU1900 12, 306
DVU1901 peptidyl-prolyl cis-trans isomerase domain-containing protein 12, 229
DVU1978 Na+/H+ antiporter family protein 223, 294
DVU2024 hypothetical protein DVU2024 273, 294
DVU2026 hypothetical protein DVU2026 273, 294
DVU2031 hypothetical protein DVU2031 273, 294
DVU2037 cobS protein 273, 294
DVU2131 hypothetical protein DVU2131 12, 291
DVU2359 sigma-54 dependent transcriptional regulator 12, 46
DVU2435 CorA family protein 12, 337
DVU3100 biopolymer ExbD/TolR family transporter 44, 294
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 DVU1585
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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