Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2023

hypothetical protein DVU2023

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2023
(Mouseover regulator name to see its description)

DVU2023 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU2023 (22)
Regulator Module Operator
DVU0679
DVUA0024
15 combiner
DVU0804
DVU3142
15 combiner
DVU1754
DVU2934
15 combiner
DVU2567 15 tf
DVU2588
DVU1967
15 combiner
DVU2686
DVU3023
15 combiner
DVU2832 15 tf
DVU3142 15 tf
DVU3142
DVU2934
15 combiner
DVUA0151
DVU0744
15 combiner
DVU1674
DVU1744
273 combiner
DVU1759 273 tf
DVU2086 273 tf
DVU2086
DVU2644
273 combiner
DVU2086
DVU3334
273 combiner
DVU2086
DVUA0100
273 combiner
DVU2097 273 tf
DVU2114
DVU3305
273 combiner
DVU2114
DVUA0100
273 combiner
DVU2251 273 tf
DVU2799
DVU1744
273 combiner
DVU3305 273 tf

Warning: DVU2023 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
29 3.20e+03 cAtacc..aAcAtAacgg..a
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RegPredict
30 1.70e+04 ACGg.CCGtTCCTGC
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RegPredict
521 1.60e-04 atCtcTAT.TTTgaAat.TAc
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RegPredict
522 1.10e-04 aTT.cAA.ctAtt.aaCAAGGa
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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 DVU2023

Warning: No Functional annotations were found!

Module neighborhood information for DVU2023

DVU2023 has total of 41 gene neighbors in modules 15, 273
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0022 HAMP domain/GGDEF domain/EAL domain-containing protein 15, 291
DVU0117 glycosyl transferase group 2 family protein 15, 82
DVU0286 hisF imidazole glycerol phosphate synthase subunit HisF 15, 65
DVU0539 sigma-54 dependent DNA-binding response regulator 15, 324
DVU0621 sigma-54 dependent DNA-binding response regulator 15, 197
DVU0681 sensor histidine kinase/response regulator 15, 291
DVU0807 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 15, 28
DVU1163 major facilitator superfamily protein 15, 144
DVU2009 hypothetical protein DVU2009 196, 273
DVU2012 hypothetical protein DVU2012 196, 273
DVU2015 hypothetical protein DVU2015 196, 273
DVU2016 GGDEF domain-containing protein 196, 273
DVU2021 hypothetical protein DVU2021 229, 273
DVU2023 hypothetical protein DVU2023 15, 273
DVU2024 hypothetical protein DVU2024 273, 294
DVU2025 hypothetical protein DVU2025 273, 326
DVU2026 hypothetical protein DVU2026 273, 294
DVU2027 hypothetical protein DVU2027 196, 273
DVU2028 hypothetical protein DVU2028 186, 273
DVU2031 hypothetical protein DVU2031 273, 294
DVU2034 hypothetical protein DVU2034 196, 273
DVU2035 plasmid stabilization system family protein 273, 344
DVU2037 cobS protein 273, 294
DVU2038 hypothetical protein DVU2038 196, 273
DVU2039 hypothetical protein DVU2039 208, 273
DVU2040 hypothetical protein DVU2040 31, 273
DVU2041 hypothetical protein DVU2041 15, 273
DVU2042 Fic family protein 62, 273
DVU2043 hypothetical protein DVU2043 270, 273
DVU2045 hypothetical protein DVU2045 196, 273
DVU2046 hypothetical protein DVU2046 273, 307
DVU2047 hypothetical protein DVU2047 196, 273
DVU2502 murB UDP-N-acetylenolpyruvoylglucosamine reductase 15, 86
DVU2661 twin-arginine translocation pathway signal sequence domain-containing protein 15, 82
DVU2736 hypothetical protein DVU2736 15, 97
DVU2906 umuC umuC protein 15, 203
DVU2994 glycosyl transferase group 2 family protein 15, 112
DVU3000 hypothetical protein DVU3000 15, 284
DVU3007 hypothetical protein DVU3007 15, 284
DVU3128 lipoprotein 15, 138
DVUA0125 Slt family transglycosylase 15, 68
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 DVU2023
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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