Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1559 mop

aldehyde oxidoreductase

CircVis
Functional Annotations (5)
Function System
Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
metal ion binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1559
(Mouseover regulator name to see its description)

DVU1559 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU1559 mop (21)
Regulator Module Operator
DVU0118 77 tf
DVU0309
DVU1964
77 combiner
DVU0309
DVU3023
77 combiner
DVU0436 77 tf
DVU0682 77 tf
DVU0682
DVU0309
77 combiner
DVU0804 77 tf
DVU1517 77 tf
DVU1561
DVU0804
77 combiner
DVU2097
DVU1561
77 combiner
DVU2394 77 tf
DVU2588
DVU2934
77 combiner
DVU2675
DVU2588
77 combiner
DVU2675
DVUA0024
77 combiner
DVU1517 242 tf
DVU1517
DVU0539
242 combiner
DVU1754 242 tf
DVU1754
DVU3305
242 combiner
DVU2588
DVU1967
242 combiner
DVU3142 242 tf
DVU3255
DVU3186
242 combiner

Warning: DVU1559 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
151 2.60e+02 caATaAtGgAaa.A
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RegPredict
152 2.40e+03 G.AAaATaAT
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RegPredict
461 0.00e+00 aa.TcTctGcAtaaGaaAaAtAat
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RegPredict
462 1.30e-03 ATTaccTCCaTCtCAcGGGaA
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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 DVU1559

DVU1559 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
metal ion binding go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for DVU1559

DVU1559 has total of 43 gene neighbors in modules 77, 242
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0018 methyl-accepting chemotaxis protein 77, 208
DVU0330 response regulator 77, 321
DVU0331 sensory box histidine kinase 77, 321
DVU0591 methyl-accepting chemotaxis protein 77, 321
DVU0592 cheW-1 chemotaxis protein CheW 77, 321
DVU0700 methyl-accepting chemotaxis protein 77, 321
DVU1162 hypothetical protein DVU1162 80, 242
DVU1414 sensory box protein 242, 299
DVU1550 phosphoglycerate mutase family protein 242, 322
DVU1551 HD domain-containing protein 242, 322
DVU1552 hypothetical protein DVU1552 77, 242
DVU1553 AMP-binding protein 242, 322
DVU1554 radical SAM domain-containing protein 110, 242
DVU1555 hypothetical protein DVU1555 242, 322
DVU1556 hypothetical protein DVU1556 242, 322
DVU1557 hypothetical protein DVU1557 242, 322
DVU1558 hypothetical protein DVU1558 242, 322
DVU1559 mop aldehyde oxidoreductase 77, 242
DVU1560 molybdopterin biosynthesis protein 242, 322
DVU1561 molybdenum-binding protein 242, 263
DVU1570 porB pyruvate ferredoxin oxidoreductase subunit beta 77, 153
DVU1753 hypothetical protein DVU1753 118, 242
DVU2020 hypothetical protein DVU2020 77, 175
DVU2075 ParA family protein 77, 144
DVU2077 hypothetical protein DVU2077 77, 102
DVU2118 hypothetical protein DVU2118 77, 321
DVU2119 type II/III secretion system protein 77, 321
DVU2121 response regulator 77, 321
DVU2126 hypothetical protein DVU2126 77, 321
DVU2281 sensor histidine kinase/response regulator 77, 321
DVU2481 formate dehydrogenase subunit beta 77, 348
DVU2483 cytochrome c family protein 77, 348
DVU2524 cytochrome c3 77, 321
DVU2525 hynB-2 periplasmic 77, 291
DVU2526 hynA-2 periplasmic 77, 321
DVU2626 hypothetical protein DVU2626 77, 321
DVU2773 hypothetical protein DVU2773 242, 326
DVU2774 hypothetical protein 208, 242
DVU3133 glycerol uptake facilitator protein 77, 321
DVU3134 glpK glycerol kinase 77, 321
DVU3246 RND efflux system outer membrane lipoprotein 77, 321
DVU3247 RND family efflux transporter MFP subunit 77, 321
DVU3265 tartrate dehydratase subunit beta 77, 205
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 DVU1559
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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