Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2554

hypothetical protein DVU2554

CircVis
Functional Annotations (1)
Function System
Uncharacterized conserved protein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2554
(Mouseover regulator name to see its description)

DVU2554 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU2554 (19)
Regulator Module Operator
DVU0813
DVU0230
119 combiner
DVU0813
DVU1517
119 combiner
DVU1572
DVU0269
119 combiner
DVU1572
DVU3255
119 combiner
DVU1788 119 tf
DVU2675
DVU3186
119 combiner
DVU2909
DVU1788
119 combiner
DVU3255
DVU1584
119 combiner
DVU0277 227 tf
DVU0277
DVU0916
227 combiner
DVU0619
DVU0230
227 combiner
DVU0744
DVU2690
227 combiner
DVU0813
DVU0230
227 combiner
DVU2086
DVU0744
227 combiner
DVU2547
DVU0230
227 combiner
DVU2567 227 tf
DVU2567
DVU0813
227 combiner
DVU2909
DVU1730
227 combiner
DVU2909
DVU2690
227 combiner

Warning: DVU2554 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
229 1.60e+03 CTgCTTGcaCggcA.gGctCGC
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RegPredict
230 1.30e+04 ATCATACATAcAA
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RegPredict
433 4.10e+03 CTGCTGaCGatG
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RegPredict
434 8.30e+03 AtcatCGcctt
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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 DVU2554

DVU2554 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized conserved protein cog/ cog
Module neighborhood information for DVU2554

DVU2554 has total of 45 gene neighbors in modules 119, 227
Gene neighbors (45)
Gene Common Name Description Module membership
DVU0093 glycosyl transferase domain-containing protein 119, 289
DVU0146 hypothetical protein DVU0146 53, 119
DVU0159 thioesterase family protein 57, 119
DVU0160 carbohydrate isomerase KpsF/GutQ family protein 57, 119
DVU0243 lipoprotein 57, 119
DVU0319 NAD-dependent epimerase/dehydratase 62, 119
DVU0359 HesB-like domain-containing protein 119, 226
DVU0380 sulfatase 119, 305
DVU0417 speA arginine decarboxylase 57, 119
DVU0418 lys1 saccharopine dehydrogenase 119, 236
DVU0525 MarR family transcriptional regulator 227, 289
DVU0759 M29 family peptidase 13, 227
DVU0825 secA preprotein translocase subunit SecA 218, 227
DVU0831 PTS system transporter subunit IID 64, 119
DVU0856 hemB delta-aminolevulinic acid dehydratase 57, 227
DVU0864 glycoprotease family protein 57, 227
DVU0865 membrane-associated zinc metalloprotease 158, 227
DVU1191 ATP-dependent protease La 57, 227
DVU1192 acylphosphatase 66, 119
DVU1193 radC DNA repair protein RadC 57, 227
DVU1267 hypothetical protein DVU1267 158, 227
DVU1432 radical SAM domain-containing protein 57, 227
DVU1467 hslU ATP-dependent protease ATP-binding subunit HslU 119, 227
DVU1722 hypothetical protein DVU1722 119, 167
DVU1788 rpoD RNA polymerase sigma-70 factor 28, 227
DVU1789 dnaG DNA primase 28, 227
DVU1855 integrase, truncation 90, 227
DVU2258 ruvC Holliday junction resolvase 65, 119
DVU2363 thiM hydroxyethylthiazole kinase 66, 227
DVU2420 hypothetical protein DVU2420 119, 236
DVU2486 acetyltransferase 119, 167
DVU2487 hypothetical protein DVU2487 66, 227
DVU2488 hypothetical protein DVU2488 66, 227
DVU2554 hypothetical protein DVU2554 119, 227
DVU2555 MATE efflux family protein 119, 120
DVU2641 lipoprotein 119, 254
DVU2658 hypothetical protein DVU2658 119, 215
DVU2659 exsB protein 119, 215
DVU2667 phosphate ABC transporter periplasmic phosphate-binding protein 119, 137
DVU2752 rhodanese-like domain-containing protein 97, 119
DVU2876 terminase large subunit 7, 119
DVU3243 dnaJ chaperone protein DnaJ 28, 227
DVU3315 pyrK dihydroorotate dehydrogenase, electron transfer subunit 66, 227
DVU3365 fmt methionyl-tRNA formyltransferase 28, 227
DVU3366 def polypeptide deformylase 227, 261
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 DVU2554
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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