Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1759

molybdenum-binding protein

CircVis
Functional Annotations (3)
Function System
N-terminal domain of molybdenum-binding protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1759
(Mouseover regulator name to see its description)

DVU1759 is regulated by 20 influences and regulates 13 modules.
Regulators for DVU1759 (20)
Regulator Module Operator
DVU0309
DVU3193
92 combiner
DVU0379 92 tf
DVU0525 92 tf
DVU0653
DVU2251
92 combiner
DVU1561 92 tf
DVU1645
DVU1518
92 combiner
DVU1645
DVU1561
92 combiner
DVU3167
DVU0309
92 combiner
DVU3167
DVU0569
92 combiner
DVU0063
DVU1760
179 combiner
DVU0118 179 tf
DVU0621 179 tf
DVU0679
DVU0118
179 combiner
DVU1331
DVU2275
179 combiner
DVU1645
DVU1331
179 combiner
DVU1760 179 tf
DVU2423
DVU1760
179 combiner
DVU2675 179 tf
DVU2989 179 tf
DVU3305 179 tf

Warning: DVU1759 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
179 1.00e-06 TGCaTctGcTtTCcTGTtgGA
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RegPredict
180 7.10e-05 AaGCGCAcAcaGTGCcaCATGgCA
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RegPredict
341 9.40e+01 gcAgAatAgctGgttCAaCaTga
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RegPredict
342 2.20e+02 GaaaCaaTcTgTaGtacGAGA
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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 DVU1759

DVU1759 is enriched for 3 functions in 3 categories.
Module neighborhood information for DVU1759

DVU1759 has total of 59 gene neighbors in modules 92, 179
Gene neighbors (59)
Gene Common Name Description Module membership
DVU0017 hypothetical protein DVU0017 92, 245
DVU0065 hypothetical protein DVU0065 44, 179
DVU0269 Rrf2 family transcriptional regulator 179, 346
DVU0354 hypothetical protein DVU0354 155, 179
DVU0455 hypothetical protein DVU0455 161, 179
DVU0504 rpsO 30S ribosomal protein S15 44, 179
DVU0602 hypothetical protein DVU0602 5, 179
DVU0605 hypothetical protein DVU0605 92, 331
DVU0696 hypothetical protein DVU0696 92, 138
DVU0705 dctM TRAP transporter subunit DctM 92, 265
DVU0706 TRAP transporter subunit DctQ 68, 92
DVU0707 dctP TRAP transporter solute receptor DctP 92, 315
DVU0708 hypothetical protein DVU0708 92, 116
DVU0709 hypothetical protein DVU0709 12, 92
DVU0909 hypothetical protein DVU0909 92, 244
DVU0914 cobS cobalamin-5-phosphate synthase 92, 160
DVU1010 hypothetical protein DVU1010 170, 179
DVU1084 pstB-1 phosphate transporter ATP-binding protein 126, 179
DVU1086 hypothetical protein DVU1086 55, 179
DVU1154 hypothetical protein DVU1154 179, 289
DVU1229 hypothetical protein DVU1229 92, 224
DVU1235 hypothetical protein DVU1235 92, 266
DVU1256 heptosyltransferase family protein 179, 313
DVU1331 LysR family transcriptional regulator 179, 279
DVU1333 hypothetical protein DVU1333 179, 279
DVU1388 hypothetical protein DVU1388 92, 225
DVU1591 hypothetical protein DVU1591 92, 116
DVU1747 hypothetical protein DVU1747 92, 243
DVU1759 molybdenum-binding protein 92, 179
DVU1777 cynT carbonic anhydrase 179, 262
DVU1971 hypothetical protein DVU1971 156, 179
DVU1994 hypothetical protein DVU1994 92, 224
DVU2002 hypothetical protein DVU2002 92, 266
DVU2073 cheY-2 chemotaxis protein CheY 179, 289
DVU2098 cooS carbon monoxide dehydrogenase 179, 262
DVU2101 hypothetical protein DVU2101 92, 312
DVU2102 OMP85 family outer membrane protein 92, 266
DVU2103 iron-sulfur cluster-binding/ATPase 92, 245
DVU2181 antirepressor 107, 179
DVU2199 hypothetical protein DVU2199 70, 92
DVU2208 hypothetical protein DVU2208 5, 179
DVU2214 hypothetical protein DVU2214 134, 179
DVU2219 hypothetical protein DVU2219 92, 224
DVU2267 hypothetical protein DVU2267 37, 179
DVU2297 glycine/betaine/L-proline ABC transporter periplasmic-binding protein 109, 179
DVU2301 lipoprotein 92, 261
DVU2319 transcriptional regulator domain-containing protein 92, 316
DVU2652 hypothetical protein DVU2652 179, 219
DVU2653 hypothetical protein DVU2653 179, 219
DVU2669 hypothetical protein DVU2669 179, 279
DVU2672 hypothetical protein DVU2672 17, 179
DVU2738 methyl-accepting chemotaxis protein 94, 179
DVU2882 folC folylpolyglutamate synthase 155, 179
DVU2911 hemolysin A 92, 134
DVU3120 hypothetical protein DVU3120 92, 127
DVU3131 transcriptional regulator 92, 321
DVU3340 hypothetical protein DVU3340 92, 239
DVU3395 M24/M37 family peptidase 29, 179
DVUA0085 hypothetical protein DVUA0085 178, 179
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 DVU1759
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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