Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1354

hypothetical protein DVU1354

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1354
(Mouseover regulator name to see its description)

DVU1354 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU1354 (17)
Regulator Module Operator
DVU0110 215 tf
DVU0936 215 tf
DVU1144 215 tf
DVU1645
DVU2644
215 combiner
DVU1690
DVU0942
215 combiner
DVU2275 215 tf
DVU2319 215 tf
DVU2644 215 tf
DVU2686 215 tf
DVU3334
DVU0110
215 combiner
DVU0539
DVU1419
309 combiner
DVU1744 309 tf
DVU2567
DVU3334
309 combiner
DVU3080 309 tf
DVU3255
DVU1744
309 combiner
DVU3334
DVU0230
309 combiner
DVUA0143 309 tf

Warning: DVU1354 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
409 5.00e+00 GtATAGattaAaT.TaT..aT
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RegPredict
410 3.90e+02 T.TTgAcaaT.AT.tGtgaTtA
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RegPredict
591 1.50e-03 Acgattcaa.gcgcaA.aaCAcAg
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RegPredict
592 8.20e-01 t.aTAgt.tTctcaaAaActa
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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 DVU1354

Warning: No Functional annotations were found!

Module neighborhood information for DVU1354

DVU1354 has total of 51 gene neighbors in modules 215, 309
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0012 hypothetical protein DVU0012 206, 309
DVU0023 hypothetical protein DVU0023 215, 283
DVU0225 hypothetical protein DVU0225 215, 255
DVU0408 response regulator/sensory box/GGDEF domain/EAL domain-containing protein 121, 309
DVU0438 AcrB/AcrD/AcrF family protein 166, 309
DVU0528 phosphatidylglycerophosphatase 309, 330
DVU0537 hypothetical protein DVU0537 225, 309
DVU0616 hypothetical protein DVU0616 46, 309
DVU0666 HD domain-containing protein 214, 309
DVU0674 His/Glu/Gln/Arg/opine ABC transporter permease 309, 332
DVU0702 cytochrome c family protein 215, 255
DVU0715 branched-chain amino acid ABC transporter ATP binding protein 215, 331
DVU0716 branched-chain amino acid ABC transporter ATP-binding protein 215, 331
DVU0745 ABC transporter periplasmic substrate-binding protein 215, 230
DVU0832 tetrapyrrole methylase family protein 215, 226
DVU0852 extracellular solute-binding protein 127, 309
DVU0965 hypothetical protein DVU0965 146, 215
DVU1006 hypothetical protein DVU1006 157, 215
DVU1057 cobalt ABC transporter permease 145, 309
DVU1177 hypothetical protein DVU1177 157, 215
DVU1225 hypothetical protein DVU1225 215, 228
DVU1232 glnB-1 nitrogen regulatory protein P-II 31, 215
DVU1354 hypothetical protein DVU1354 215, 309
DVU1425 gcvPA glycine dehydrogenase subunit 1 14, 309
DVU1473 hypothetical protein DVU1473 155, 309
DVU1578 hypothetical protein 215, 226
DVU1588 hpt hypoxanthine phosphoribosyltransferase 215, 294
DVU1632 PTS system transporter subunit IIA 309, 330
DVU1669 rluB ribosomal large subunit pseudouridine synthase B 215, 337
DVU1708 hypothetical protein DVU1708 215, 244
DVU1709 hsdM type I restriction-modification system, M subunit 215, 244
DVU1873 ppiB-2 peptidyl-prolyl cis-trans isomerase B 215, 254
DVU1877 polysaccharide deacetylase family protein 63, 215
DVU1989 hypothetical protein DVU1989 214, 309
DVU2206 hypothetical protein DVU2206 78, 215
DVU2235 hypothetical protein DVU2235 215, 308
DVU2261 hypothetical protein DVU2261 57, 309
DVU2308 hypothetical protein DVU2308 215, 332
DVU2527 transcriptional regulator 215, 224
DVU2657 6-pyruvoyl tetrahydrobiopterin synthase 215, 279
DVU2658 hypothetical protein DVU2658 119, 215
DVU2659 exsB protein 119, 215
DVU2745 hypothetical protein DVU2745 263, 309
DVU2746 hypothetical protein DVU2746 225, 309
DVU2778 hypothetical protein DVU2778 215, 263
DVU2845 HIT family protein 90, 309
DVU2940 hypothetical protein DVU2940 146, 215
DVU2941 hypothetical protein DVU2941 215, 226
DVU3144 cytochrome c family protein 309, 321
DVU3145 hydrogenase, b-type cytochrome subunit 214, 309
DVU3380 hypothetical protein DVU3380 309, 330
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 DVU1354
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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