Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2671

phosphodiesterase

CircVis
Functional Annotations (4)
Function System
Predicted HD superfamily hydrolase cog/ cog
RNA binding go/ molecular_function
catalytic activity go/ molecular_function
HDIG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2671
(Mouseover regulator name to see its description)

DVU2671 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU2671 (22)
Regulator Module Operator
DVU0629 121 tf
DVU1744 121 tf
DVU2036
DVU2097
121 combiner
DVU2114
DVUA0100
121 combiner
DVU2547 121 tf
DVU2547
DVU0539
121 combiner
DVU2827 121 tf
DVU3080 121 tf
DVU3080
DVU1744
121 combiner
DVU1561
DVU0118
5 combiner
DVU1572
DVU2423
5 combiner
DVU1572
DVU3313
5 combiner
DVU1730 5 tf
DVU1745 5 tf
DVU1759 5 tf
DVU1759
DVU2275
5 combiner
DVU2111
DVU1964
5 combiner
DVU2275 5 tf
DVU2275
DVU0057
5 combiner
DVU2423
DVU3313
5 combiner
DVU2557 5 tf
DVU2989 5 tf

Warning: DVU2671 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
9 6.40e+00 cTtgtttG.AAG.gaaTaaat.ga
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RegPredict
10 2.30e+03 CtCACaCCACAaAC
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RegPredict
233 1.70e+01 gAtAtTCAaGAAaga.gaaT
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RegPredict
234 2.20e+03 ttcaaTTGaa.tga.Aa.TG
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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 DVU2671

DVU2671 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted HD superfamily hydrolase cog/ cog
RNA binding go/ molecular_function
catalytic activity go/ molecular_function
HDIG tigr/ tigrfam
Module neighborhood information for DVU2671

DVU2671 has total of 60 gene neighbors in modules 5, 121
Gene neighbors (60)
Gene Common Name Description Module membership
DVU0036 hypothetical protein DVU0036 5, 103
DVU0052 era GTP-binding protein Era 5, 30
DVU0057 TetR family transcriptional regulator 5, 316
DVU0060 RND family efflux transporter MFP subunit 5, 94
DVU0061 multidrug resistance protein 5, 94
DVU0062 RND efflux system outer membrane lipoprotein 5, 94
DVU0063 MarR family transcriptional regulator 5, 94
DVU0064 hypothetical protein DVU0064 5, 323
DVU0085 trpB-1 tryptophan synthase subunit beta 5, 95
DVU0196 hypothetical protein DVU0196 78, 121
DVU0408 response regulator/sensory box/GGDEF domain/EAL domain-containing protein 121, 309
DVU0563 ISD1, transposase OrfB 18, 121
DVU0602 hypothetical protein DVU0602 5, 179
DVU0603 hypothetical protein DVU0603 5, 94
DVU0802 hypothetical protein DVU0802 33, 121
DVU0872 glycosyl transferase group 2 family protein 5, 55
DVU0993 hypothetical protein DVU0993 33, 121
DVU1009 hypothetical protein DVU1009 5, 30
DVU1171 hypothetical protein DVU1171 121, 126
DVU1367 tatA twin arginine translocase protein A 121, 232
DVU1387 hypothetical protein DVU1387 121, 258
DVU1454 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 5, 278
DVU1571 rho transcription termination factor Rho 5, 235
DVU1617 nitroreductase family protein 5, 323
DVU1618 iojap-like protein 5, 323
DVU1619 gpmA phosphoglyceromutase 5, 323
DVU1739 hypothetical protein DVU1739 121, 214
DVU1750 hypothetical protein DVU1750 121, 246
DVU1773 hypothetical protein DVU1773 11, 121
DVU1851 M24/M37 family peptidase 5, 16
DVU1995 anti-anti-sigma factor 121, 246
DVU2017 ISDvu5, transposase 121, 219
DVU2068 HD domain-containing protein 121, 342
DVU2130 hypothetical protein DVU2130 5, 94
DVU2148 hypothetical protein DVU2148 5, 316
DVU2178 ISDvu2, transposase OrfB 121, 233
DVU2208 hypothetical protein DVU2208 5, 179
DVU2263 outer membrane autotransporter 121, 230
DVU2274 hypothetical protein DVU2274 5, 44
DVU2284 hypothetical protein DVU2284 5, 275
DVU2299 glycine/betaine/L-proline ABC transporter ATP binding protein 5, 235
DVU2634 hypothetical protein DVU2634 5, 9
DVU2671 phosphodiesterase 5, 121
DVU2682 DedA family protein 121, 344
DVU2842 type II DNA modification methyltransferase 121, 154
DVU2904 ribosomal RNA large subunit methyltransferase N 5, 64
DVU3038 hypothetical protein DVU3038 33, 121
DVU3138 hypothetical protein DVU3138 121, 219
DVU3151 tRNA modifying protein 5, 94
DVU3194 engA GTP-binding protein EngA 5, 94
DVU3204 purA adenylosuccinate synthetase 5, 94
DVU3205 transglycosylase 5, 94
DVU3206 phosphoribosylaminoimidazolecarboxamide formyltransferase 5, 235
DVU3212 pyridine nucleotide-disulfide oxidoreductase 5, 236
DVU3218 pncA pyrazinamidase/nicotinamidase 121, 122
DVU3313 LysR family transcriptional regulator 5, 279
DVUA0018 hypothetical protein DVUA0018 121, 233
DVUA0067 hypothetical protein DVUA0067 121, 187
DVUA0071 glycosyl transferase, group 1/2 family protein 16, 121
DVUA0135 CRISPR-associated Cas2 family protein 121, 150
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 DVU2671
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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