Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0049

OmpA family protein

CircVis
Functional Annotations (4)
Function System
Flagellar motor protein cog/ cog
cell outer membrane go/ cellular_component
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0049
(Mouseover regulator name to see its description)

DVU0049 is regulated by 14 influences and regulates 0 modules.
Regulators for DVU0049 (14)
Regulator Module Operator
DVU0653
DVU1690
247 combiner
DVU0744
DVU2690
247 combiner
DVU1402
DVU1730
247 combiner
DVU1572
DVU0936
247 combiner
DVU1730 247 tf
DVU2423
DVU0619
247 combiner
DVU3381
DVU1730
247 combiner
DVU0606
DVU0269
222 combiner
DVU1584 222 tf
DVU1584
DVU0269
222 combiner
DVU2086
DVU0744
222 combiner
DVU2086
DVU3229
222 combiner
DVU2423
DVU0744
222 combiner
DVU2532 222 tf

Warning: DVU0049 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
423 4.80e-02 AataGACaTATaTGaAcTaaTGaA
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RegPredict
424 3.70e-03 actCctCcGtaaatcTgCacG
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RegPredict
471 6.60e-03 at.ttAcAtT.ttaTaTgaa
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RegPredict
472 3.50e+02 ta.Aaaaa.aCAaAt
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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 DVU0049

DVU0049 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Flagellar motor protein cog/ cog
cell outer membrane go/ cellular_component
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
Module neighborhood information for DVU0049

DVU0049 has total of 49 gene neighbors in modules 222, 247
Gene neighbors (49)
Gene Common Name Description Module membership
DVU0026 hypothetical protein DVU0026 247, 261
DVU0049 OmpA family protein 222, 247
DVU0094 methyl-accepting chemotaxis protein 247, 289
DVU0100 TonB-dependent receptor 247, 256
DVU0101 UbiE/COQ5 family methlytransferase 69, 247
DVU0103 cation ABC transporter ATP-binding protein 247, 334
DVU0130 phosphoglycolate phosphatase 185, 247
DVU0131 hypothetical protein DVU0131 167, 222
DVU0132 hypothetical protein DVU0132 167, 222
DVU0133 hypothetical protein DVU0133 167, 222
DVU0195 hypothetical protein DVU0195 222, 314
DVU0233 hypothetical protein DVU0233 247, 281
DVU0288 None 107, 222
DVU0355 sensory box protein 222, 320
DVU0360 ilvB-1 acetolactate synthase catalytic subunit 99, 247
DVU0446 sodium/solute symporter family protein 247, 334
DVU0452 hypothetical protein DVU0452 106, 222
DVU0533 hmc operon protein 4 189, 247
DVU0534 hmc operon protein 3 189, 247
DVU0588 formate dehydrogenase subunit beta 189, 247
DVU0593 L-lysine exporter 53, 247
DVU0623 hypothetical protein DVU0623 134, 222
DVU0644 hypothetical protein DVU0644 99, 222
DVU0678 hypothetical protein DVU0678 53, 247
DVU0791 methylated DNA-protein cysteine methyltransferase DNA binding subunit 247, 267
DVU1838 trxB-2 thioredoxin-disulfide reductase 167, 222
DVU2090 EF hand domain-containing protein 46, 247
DVU2570 GGDEF domain/HAMP domain-containing protein 69, 247
DVU2687 hypothetical protein DVU2687 247, 269
DVU2730 tail fiber protein 181, 247
DVU2825 pyruvate formate-lyase 1 activating enzyme 214, 222
DVU2829 hypothetical protein DVU2829 38, 247
DVU2849 tail fiber protein 247, 314
DVU2884 aminopeptidase 1 62, 222
DVU2992 glycosyl transferase group 2 family protein 222, 341
DVU2999 methionyl-tRNA formyltransferase 247, 271
DVU3064 sensory box protein 176, 222
DVU3106 GGDEF domain-containing protein 36, 222
DVU3244 hypothetical protein DVU3244 247, 289
DVU3321 hypothetical protein DVU3321 185, 222
DVU3322 hypothetical protein DVU3322 144, 222
DVU3323 ABC transporter permease 144, 222
DVU3324 ABC transporter ATP-binding protein 144, 222
DVU3372 hypothetical protein DVU3372 247, 311
DVU3384 zraP zinc resistance-associated protein 53, 247
DVU3386 permease 69, 222
DVUA0029 hypothetical protein DVUA0029 167, 222
DVUA0036 TPR domain-containing protein 53, 247
DVUA0089 hypothetical protein DVUA0089 90, 247
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 DVU0049
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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