Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0075

radical SAM domain-containing protein

CircVis
Functional Annotations (3)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0075
(Mouseover regulator name to see its description)

DVUA0075 is regulated by 16 influences and regulates 0 modules.
Regulators for DVUA0075 (16)
Regulator Module Operator
DVU0230 337 tf
DVU1584
DVU0653
337 combiner
DVU1584
DVU1690
337 combiner
DVU2114
DVUA0100
337 combiner
DVU2423 337 tf
DVU2644
DVU0936
337 combiner
DVU2644
DVU2532
337 combiner
DVU2819
DVU0230
337 combiner
DVU0525 255 tf
DVU0936 255 tf
DVU0946
DVU2114
255 combiner
DVU2836
DVU0653
255 combiner
DVU3186
DVU0942
255 combiner
DVU3186
DVU2394
255 combiner
DVU3186
DVUA0100
255 combiner
DVU3193 255 tf

Warning: DVUA0075 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
485 2.90e+00 TTTTTTaCtgC
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RegPredict
486 3.50e+03 T.TCgtATtcATGCA
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RegPredict
639 7.30e+02 AAGCCTcGaaG
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RegPredict
640 1.30e+04 CaaAAGgA
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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 DVUA0075

DVUA0075 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for DVUA0075

DVUA0075 has total of 43 gene neighbors in modules 255, 337
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0073 CDP-glucose-4,6-dehydratase 331, 337
DVU0105 glutamine ABC transporter ATP-binding protein 78, 255
DVU0107 glnH glutamine ABC transporter periplasmic glutamine-binding protein 221, 255
DVU0184 hypothetical protein DVU0184 162, 337
DVU0225 hypothetical protein DVU0225 215, 255
DVU0226 hypothetical protein DVU0226 50, 255
DVU0227 hypothetical protein DVU0227 63, 255
DVU0356 tag DNA-3-methyladenine glycosylase I 255, 308
DVU0357 hypothetical protein DVU0357 6, 255
DVU0474 ISDvu4, transposase 257, 337
DVU0500 selB selenocysteine-specific translation elongation factor 157, 255
DVU0547 high-affinity branched chain amino acid ABC transporter periplasmic branched chain amino acid-binding protein 255, 342
DVU0624 NapC/NirT cytochrome c family protein 153, 255
DVU0625 cytochrome c nitrite reductase, catalytic subunit NfrA 153, 255
DVU0702 cytochrome c family protein 215, 255
DVU0767 class V aminotransferase 150, 337
DVU1238 amino acid ABC transporter periplasmic amino acid-binding protein 146, 255
DVU1266 hypothetical protein DVU1266 172, 337
DVU1290 nitrate reductase subunit gamma 255, 344
DVU1567 hypothetical protein DVU1567 226, 337
DVU1599 crcB crcB protein 65, 337
DVU1669 rluB ribosomal large subunit pseudouridine synthase B 215, 337
DVU1844 septum formation initiator family protein 318, 337
DVU1845 hypothetical protein DVU1845 332, 337
DVU1944 pyruvate ferredoxin oxidoreductase, iron-sulfur binding subunit 150, 337
DVU1945 2-oxoglutarate ferredoxin oxidoreductase subunit alpha 250, 337
DVU1946 2-oxoglutarate ferredoxin oxidoreductase subunit beta 250, 337
DVU1947 pyruvate ferredoxin oxidoreductase subunit gamma 190, 337
DVU1948 hypothetical protein DVU1948 190, 337
DVU2048 hypothetical protein DVU2048 337, 339
DVU2049 None 196, 337
DVU2200 hypothetical protein DVU2200 171, 255
DVU2205 tryptophan-specific transport protein 255, 262
DVU2407 hypothetical protein DVU2407 216, 255
DVU2435 CorA family protein 12, 337
DVU2582 TetR family transcriptional regulator 166, 337
DVU3173 hypothetical protein DVU3173 147, 337
DVU3275 hypothetical protein DVU3275 29, 337
DVU3277 hypothetical protein DVU3277 146, 337
DVUA0006 magnesium transporter MgtE 163, 255
DVUA0072 glycosyl transferase, group 1 family protein 255, 304
DVUA0073 asparagine synthase (glutamine-hydrolyzing) 255, 337
DVUA0075 radical SAM domain-containing protein 255, 337
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 DVUA0075
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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