Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0394

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 DVU0394
(Mouseover regulator name to see its description)

DVU0394 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU0394 (17)
Regulator Module Operator
DVU0110 62 tf
DVU0309
DVU1340
62 combiner
DVU0309
DVU1547
62 combiner
DVU0309
DVU3023
62 combiner
DVU1517 62 tf
DVU1561
DVU1584
62 combiner
DVU2547
DVU1730
62 combiner
DVU2567
DVU2675
62 combiner
DVU2960
DVU1730
62 combiner
DVU3080 62 tf
DVU3167 62 tf
DVUA0024 62 tf
DVU1730 99 tf
DVU2423
DVU3381
99 combiner
DVU2644
DVU1584
99 combiner
DVU3255
DVU1584
99 combiner
DVUA0151
DVU1730
99 combiner

Warning: DVU0394 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
121 1.70e-05 aattt.atGCcAGCCcTA.AGT
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RegPredict
122 3.60e+00 atAcaAaGATcAtTTTaT
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RegPredict
191 0.00e+00 aagT.tTcacagctTCtgcCGATa
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RegPredict
192 4.00e-02 ATtgtgAtACtTtaCccATtG
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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 DVU0394

DVU0394 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 DVU0394

DVU0394 has total of 53 gene neighbors in modules 62, 99
Gene neighbors (53)
Gene Common Name Description Module membership
DVU0020 hypothetical protein DVU0020 99, 314
DVU0140 response regulator 37, 99
DVU0148 lipoprotein 53, 99
DVU0149 hypothetical protein DVU0149 53, 99
DVU0150 hypothetical protein DVU0150 53, 99
DVU0151 HAMP domain/sigma-54 interaction domain-containing protein 17, 99
DVU0152 phosphoenolpyruvate synthase-like protein 53, 99
DVU0231 hypothetical protein DVU0231 99, 106
DVU0232 hypothetical protein DVU0232 37, 99
DVU0247 response regulator 35, 62
DVU0250 hypothetical protein DVU0250 62, 280
DVU0319 NAD-dependent epimerase/dehydratase 62, 119
DVU0325 hypD hydrogenase expression/formation protein HypD 22, 62
DVU0349 NeuB family protein 62, 250
DVU0358 hypothetical protein DVU0358 37, 99
DVU0360 ilvB-1 acetolactate synthase catalytic subunit 99, 247
DVU0361 acetolactate synthase 1 regulatory subunit 99, 205
DVU0391 hypothetical protein DVU0391 99, 161
DVU0394 radical SAM domain-containing protein 62, 99
DVU0499 hypothetical protein DVU0499 46, 62
DVU0523 flgM negative regulator of flagellin synthesis FlgM 62, 122
DVU0524 hypothetical protein DVU0524 62, 122
DVU0644 hypothetical protein DVU0644 99, 222
DVU0672 hypothetical protein DVU0672 99, 230
DVU0800 hypothetical protein DVU0800 62, 225
DVU0976 response regulator 99, 122
DVU0977 hypothetical protein DVU0977 99, 122
DVU0989 periplasmic divalent cation tolerance protein cutA 57, 99
DVU1072 hypothetical protein DVU1072 99, 236
DVU1073 hypothetical protein DVU1073 99, 122
DVU1259 hypothetical protein DVU1259 46, 99
DVU1670 hypothetical protein DVU1670 53, 62
DVU1824 hypothetical protein DVU1824 27, 99
DVU1868 dapA dihydrodipicolinate synthase 62, 236
DVU1953 proA gamma-glutamyl phosphate reductase 46, 62
DVU2042 Fic family protein 62, 273
DVU2082 flagellin 62, 236
DVU2095 thiS thiamine biosynthesis protein ThiS 99, 345
DVU2100 universal stress protein 66, 99
DVU2203 L-PSP family endoribonuclease 62, 236
DVU2446 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase 62, 115
DVU2475 ferredoxin-NADP(+) reductase subunit alpha 46, 62
DVU2666 phosphate ABC transporter permease 99, 214
DVU2735 paaK-3 phenylacetate-coenzyme A ligase 62, 236
DVU2756 radical SAM domain-containing protein 62, 278
DVU2883 selA selenocysteine synthase 62, 162
DVU2884 aminopeptidase 1 62, 222
DVU2897 hypothetical protein DVU2897 62, 277
DVU2948 flagellin N-terminal domain-containing protein 62, 122
DVU3068 GAF domain/sensory box/EAL domain-containing protein 35, 62
DVU3073 hypothetical protein DVU3073 99, 211
DVU3208 membrane protein 62, 223
DVU3364 hypothetical protein DVU3364 35, 62
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 DVU0394
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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