Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0896

NLP/P60 family lipoprotein

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0896
(Mouseover regulator name to see its description)

DVU0896 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU0896 (21)
Regulator Module Operator
DVU0057 146 tf
DVU0230 146 tf
DVU0525 146 tf
DVU0606
DVU1690
146 combiner
DVU1730 146 tf
DVU1745 146 tf
DVU2423
DVU0619
146 combiner
DVU2423
DVU1402
146 combiner
DVU2557
DVU1690
146 combiner
DVU2686 146 tf
DVU3193
DVU1690
146 combiner
DVU0946
DVU1690
78 combiner
DVU1547
DVU3142
78 combiner
DVU1690 78 tf
DVU2086
DVU0539
78 combiner
DVU2423
DVU2588
78 combiner
DVU3142
DVU0813
78 combiner
DVU3186
DVU1584
78 combiner
DVU3186
DVU2275
78 combiner
DVU3255
DVU2644
78 combiner
DVU3255
DVU2799
78 combiner

Warning: DVU0896 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
153 6.20e+01 tAGca.caaAgg.ggcGg.tgtAA
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RegPredict
154 1.10e+02 tCaaGacaAaCGgtGcaaGgc
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RegPredict
279 5.10e-02 GcCaGcttcTACcGGa
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RegPredict
280 8.10e+04 C.ataCgc.T.tacTc.GtgAcgg
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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 DVU0896

Warning: No Functional annotations were found!

Module neighborhood information for DVU0896

DVU0896 has total of 53 gene neighbors in modules 78, 146
Gene neighbors (53)
Gene Common Name Description Module membership
DVU0014 infA translation initiation factor IF-1 78, 344
DVU0041 Slt family transglycosylase 145, 146
DVU0054 dihydrouridine synthase family protein 56, 78
DVU0105 glutamine ABC transporter ATP-binding protein 78, 255
DVU0158 hypothetical protein DVU0158 17, 78
DVU0196 hypothetical protein DVU0196 78, 121
DVU0415 pepA cytosol aminopeptidase 54, 78
DVU0793 hypothetical protein DVU0793 78, 164
DVU0841 aspartate aminotransferase 146, 344
DVU0895 RecD/TraA family helicase 75, 78
DVU0896 NLP/P60 family lipoprotein 78, 146
DVU0899 hypothetical protein DVU0899 146, 172
DVU0936 hypothetical protein DVU0936 146, 232
DVU0965 hypothetical protein DVU0965 146, 215
DVU0966 amino acid ABC transporter periplasmic amino acid-binding protein 146, 306
DVU1008 hypothetical protein DVU1008 78, 344
DVU1033 competence/damage-inducible protein CinA protein, truncation 18, 78
DVU1038 hisA 1-(5-phosphoribosyl)-5- 146, 288
DVU1041 tatC Sec-independent protein translocase TatC 78, 164
DVU1064 aconitate hydratase 14, 146
DVU1067 Bmp family membrane protein 146, 221
DVU1074 rpmH 50S ribosomal protein L34 18, 78
DVU1238 amino acid ABC transporter periplasmic amino acid-binding protein 146, 255
DVU1245 ABC transporter ATP-binding protein 78, 347
DVU1392 NLP/P60 family protein 146, 232
DVU1406 purM phosphoribosylaminoimidazole synthetase 88, 146
DVU1423 lpdA 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase 14, 146
DVU1533 miaA tRNA delta(2)-isopentenylpyrophosphate transferase 78, 187
DVU1615 paaK-2 phenylacetate-coenzyme A ligase 146, 323
DVU1893 ATP-dependent protease 29, 78
DVU1910 YjeF-like protein 146, 249
DVU1954 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase 56, 146
DVU1990 hypothetical protein DVU1990 146, 196
DVU2056 hypothetical protein DVU2056 54, 146
DVU2150 dnaK suppressor protein 146, 297
DVU2206 hypothetical protein DVU2206 78, 215
DVU2222 ssb single-strand binding protein 18, 78
DVU2223 hypothetical protein DVU2223 50, 78
DVU2225 acetyl-CoA carboxylase, carboxyl transferase, alpha/subunit beta 64, 78
DVU2229 motA-2 chemotaxis protein MotA 78, 170
DVU2230 deoD purine nucleoside phosphorylase 17, 78
DVU2251 DNA-binding protein 135, 146
DVU2341 amino acid ABC transporter permease 78, 347
DVU2364 class I/II aminotransferase 146, 262
DVU2782 hypothetical protein DVU2782 26, 146
DVU2783 hypothetical protein DVU2783 146, 195
DVU2791 cytochrome c family protein 139, 146
DVU2940 hypothetical protein DVU2940 146, 215
DVU3056 hypothetical protein DVU3056 78, 251
DVU3171 cytochrome c3 146, 262
DVU3187 hup-4 DNA-binding protein HU 146, 232
DVU3238 response regulator 146, 157
DVU3277 hypothetical protein DVU3277 146, 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 DVU0896
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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