Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0097

radical SAM domain-containing protein

CircVis
Functional Annotations (3)
Function System
catalytic activity go/ molecular_function
metal ion binding go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0097
(Mouseover regulator name to see its description)

DVUA0097 is regulated by 22 influences and regulates 0 modules.
Regulators for DVUA0097 (22)
Regulator Module Operator
DVU0744 201 tf
DVU0813 201 tf
DVU1340
DVU2690
201 combiner
DVU1584
DVU0269
201 combiner
DVU2086 201 tf
DVU2106 201 tf
DVU2195 201 tf
DVU2275 201 tf
DVU2423
DVU0619
201 combiner
DVU2423
DVU0744
201 combiner
DVU3381 201 tf
DVUA0151
DVU1340
201 combiner
DVU0269
DVU2633
211 combiner
DVU0309
DVU0744
211 combiner
DVU0309
DVU3142
211 combiner
DVU1572
DVU0936
211 combiner
DVU1572
DVU2106
211 combiner
DVU2423
DVU0621
211 combiner
DVU2567
DVU0621
211 combiner
DVU2686
DVU3255
211 combiner
DVU2909
DVU0621
211 combiner
DVU3186
DVU2106
211 combiner

Warning: DVUA0097 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
385 1.90e+03 agGcCacGAcGcCCatctTTG
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RegPredict
386 1.00e+04 ttTCAGGaGat
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RegPredict
403 1.30e+00 tGccgTG.CtGacg
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RegPredict
404 2.90e+04 agGgCAtCcgtCccG
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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 DVUA0097

DVUA0097 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
catalytic activity go/ molecular_function
metal ion binding go/ molecular_function
4 iron, 4 sulfur cluster binding go/ molecular_function
Module neighborhood information for DVUA0097

DVUA0097 has total of 46 gene neighbors in modules 201, 211
Gene neighbors (46)
Gene Common Name Description Module membership
DVU0031 AzlC family protein 38, 211
DVU0032 hypothetical protein DVU0032 112, 211
DVU0069 hypothetical protein DVU0069 193, 201
DVU0256 DEAD-box ATP dependent DNA helicase 194, 201
DVU0393 ung uracil-DNA glycosylase 51, 211
DVU0396 hup-1 DNA-binding protein HU 194, 201
DVU0647 iron compound ABC transporter periplasmic iron compount-binding protein 23, 211
DVU0655 phosphotransferase domain-containing protein 201, 211
DVU0757 hypothetical protein DVU0757 28, 211
DVU0803 sensor histidine kinase 198, 201
DVU0814 bacterioferritin comigratory protein 112, 211
DVU0963 7-cyano-7-deazaguanine reductase 194, 201
DVU0978 ABC transporter periplasmic substrate-binding protein 76, 211
DVU0982 hypothetical protein DVU0982 57, 211
DVU1030 universal stress protein 105, 201
DVU1188 hypothetical protein DVU1188 211, 304
DVU1401 hypothetical protein DVU1401 57, 211
DVU1410 hypothetical protein DVU1410 27, 201
DVU1437 hypothetical protein DVU1437 201, 211
DVU1438 cobyrinic acid a,c-diamide synthase family protein 115, 201
DVU1445 flagellar hook-length control domain-containing protein 211, 311
DVU1938 hypothetical protein DVU1938 208, 211
DVU2005 hypothetical protein DVU2005 175, 201
DVU2419 hypothetical protein DVU2419 211, 260
DVU2477 pstS phosphate ABC transporter periplasmic phosphate-binding protein PstS 211, 304
DVU2479 phosphate ABC transporter permease 211, 304
DVU2547 transcriptional regulator 194, 201
DVU2549 hypothetical protein DVU2549 193, 201
DVU2550 hypothetical protein DVU2550 193, 201
DVU2822 TRAP transporter solute receptor DctP 82, 211
DVU2824 formate acetyltransferase 82, 211
DVU2894 sigma-54 dependent transcriptional regulator 115, 201
DVU3014 asparagine synthetase, glutamine-hydrolyzing 22, 211
DVU3073 hypothetical protein DVU3073 99, 211
DVU3209 hypothetical protein DVU3209 112, 211
DVU3213 hypothetical protein DVU3213 175, 201
DVU3219 hypothetical protein DVU3219 211, 254
DVU3223 aspB aspartate aminotransferase 211, 278
DVU3284 L-lactate permease 211, 311
DVU3337 kdpC K+-transporting ATPase subunit C 13, 201
DVU3360 ParB family protein 76, 211
DVU3361 ADP-heptose synthase 211, 278
DVUA0086 response regulator 131, 211
DVUA0097 radical SAM domain-containing protein 201, 211
DVUA0114 hypothetical protein DVUA0114 136, 211
DVUA0117 escJ type III secretion lipoprotein 136, 211
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 DVUA0097
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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